Starting phenix.real_space_refine on Tue Aug 4 23:37:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwa_54305/08_2026/9rwa_54305.map" } resolution = 3.9 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 P 94 5.49 5 S 27 5.16 5 C 4303 2.51 5 N 1278 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7379 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 355 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 351 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1220 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3473 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 7, 'TYR:plan': 2, 'ASP:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 8, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "E" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 990 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 26} Link IDs: {'rna2p': 2, 'rna3p': 44} Chain breaks: 1 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 990 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 26} Link IDs: {'rna2p': 2, 'rna3p': 44} Chain breaks: 1 Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7379 At special positions: 0 Unit cell: (90.09, 93.73, 151.97, 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 27 16.00 P 94 15.00 O 1677 8.00 N 1278 7.00 C 4303 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: 0.67 Conformation dependent library (CDL) restraints added in 308.5 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 70.2% alpha, 7.8% beta 36 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 removed outlier: 3.904A pdb=" N ARG A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.919A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.950A pdb=" N TYR C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.517A pdb=" N PHE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.594A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 130 through 137 removed outlier: 3.537A pdb=" N ILE C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'D' and resid 3 through 25 removed outlier: 3.916A 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 111 removed outlier: 3.625A pdb=" N TYR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.874A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.858A pdb=" N ILE D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 150 Processing helix chain 'D' and resid 521 through 529 removed outlier: 3.552A pdb=" N LEU D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 4.219A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.560A pdb=" N VAL D 605 " --> pdb=" O GLY D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 629 removed outlier: 4.455A 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 removed outlier: 3.562A pdb=" N TYR D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 680 removed outlier: 3.791A pdb=" N LYS D 678 " --> pdb=" O ASN D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 688 Processing helix chain 'D' and resid 690 through 694 removed outlier: 4.401A pdb=" N LYS D 694 " --> pdb=" O PHE D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 713 removed outlier: 4.295A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 removed outlier: 3.569A pdb=" N ILE D 725 " --> pdb=" O LEU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 744 removed outlier: 4.622A pdb=" N GLN D 744 " --> pdb=" O GLN D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.617A pdb=" N ILE D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 786 Processing helix chain 'D' and resid 787 through 790 Processing helix chain 'D' and resid 793 through 801 Processing helix chain 'D' and resid 803 through 816 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533 removed outlier: 3.825A pdb=" N GLU D 584 " --> pdb=" O THR D 580 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE D 573 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 565 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE D 637 " --> pdb=" O VAL D 611 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1375 1.33 - 1.45: 2186 1.45 - 1.57: 3886 1.57 - 1.69: 184 1.69 - 1.81: 44 Bond restraints: 7675 Sorted by residual: bond pdb=" CA ARG D 47 " pdb=" C ARG D 47 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.27e-02 6.20e+03 2.33e+01 bond pdb=" N1 C F 28 " pdb=" C6 C F 28 " ideal model delta sigma weight residual 1.367 1.384 -0.017 6.00e-03 2.78e+04 8.50e+00 bond pdb=" N1 C F 8 " pdb=" C6 C F 8 " ideal model delta sigma weight residual 1.367 1.384 -0.017 6.00e-03 2.78e+04 8.43e+00 bond pdb=" N1 C F 30 " pdb=" C6 C F 30 " ideal model delta sigma weight residual 1.367 1.384 -0.017 6.00e-03 2.78e+04 8.02e+00 bond pdb=" N1 C F 46 " pdb=" C6 C F 46 " ideal model delta sigma weight residual 1.367 1.384 -0.017 6.00e-03 2.78e+04 7.59e+00 ... (remaining 7670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 10128 1.65 - 3.30: 612 3.30 - 4.94: 54 4.94 - 6.59: 12 6.59 - 8.24: 2 Bond angle restraints: 10808 Sorted by residual: angle pdb=" O4' C F 42 " pdb=" C1' C F 42 " pdb=" N1 C F 42 " ideal model delta sigma weight residual 108.50 116.74 -8.24 7.00e-01 2.04e+00 1.39e+02 angle pdb=" O4' U F 40 " pdb=" C1' U F 40 " pdb=" N1 U F 40 " ideal model delta sigma weight residual 108.50 114.40 -5.90 7.00e-01 2.04e+00 7.11e+01 angle pdb=" O5' U F 9 " pdb=" C5' U F 9 " pdb=" C4' U F 9 " ideal model delta sigma weight residual 109.40 115.17 -5.77 8.00e-01 1.56e+00 5.20e+01 angle pdb=" O4' U F 41 " pdb=" C1' U F 41 " pdb=" N1 U F 41 " ideal model delta sigma weight residual 108.50 113.42 -4.92 7.00e-01 2.04e+00 4.94e+01 angle pdb=" C5' U F 40 " pdb=" C4' U F 40 " pdb=" O4' U F 40 " ideal model delta sigma weight residual 109.80 115.48 -5.68 9.00e-01 1.23e+00 3.98e+01 ... (remaining 10803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.12: 4331 26.12 - 52.24: 332 52.24 - 78.35: 114 78.35 - 104.47: 14 104.47 - 130.59: 2 Dihedral angle restraints: 4793 sinusoidal: 2677 harmonic: 2116 Sorted by residual: dihedral pdb=" O4' C F 42 " pdb=" C2' C F 42 " pdb=" C1' C F 42 " pdb=" C3' C F 42 " ideal model delta sinusoidal sigma weight residual 25.00 -9.21 34.21 1 8.00e+00 1.56e-02 2.60e+01 dihedral pdb=" C4' C F 42 " pdb=" O4' C F 42 " pdb=" C1' C F 42 " pdb=" C2' C F 42 " ideal model delta sinusoidal sigma weight residual 3.00 -30.62 33.62 1 8.00e+00 1.56e-02 2.51e+01 dihedral pdb=" C4' U F 41 " pdb=" O4' U F 41 " pdb=" C1' U F 41 " pdb=" C2' U F 41 " ideal model delta sinusoidal sigma weight residual 3.00 -18.91 21.91 1 8.00e+00 1.56e-02 1.08e+01 ... (remaining 4790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 955 0.040 - 0.079: 206 0.079 - 0.119: 132 0.119 - 0.158: 35 0.158 - 0.198: 5 Chirality restraints: 1333 Sorted by residual: chirality pdb=" C3' U F 18 " pdb=" C4' U F 18 " pdb=" O3' U F 18 " pdb=" C2' U F 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" C3' A F 44 " pdb=" C4' A F 44 " pdb=" O3' A F 44 " pdb=" C2' A F 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C2' U F 18 " pdb=" C3' U F 18 " pdb=" O2' U F 18 " pdb=" C1' U F 18 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1330 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C F 42 " -0.149 2.00e-02 2.50e+03 7.06e-02 1.12e+02 pdb=" N1 C F 42 " 0.081 2.00e-02 2.50e+03 pdb=" C2 C F 42 " 0.030 2.00e-02 2.50e+03 pdb=" O2 C F 42 " 0.031 2.00e-02 2.50e+03 pdb=" N3 C F 42 " 0.016 2.00e-02 2.50e+03 pdb=" C4 C F 42 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C F 42 " -0.103 2.00e-02 2.50e+03 pdb=" C5 C F 42 " 0.030 2.00e-02 2.50e+03 pdb=" C6 C F 42 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A F 16 " -0.083 2.00e-02 2.50e+03 3.52e-02 3.41e+01 pdb=" N9 A F 16 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A F 16 " 0.031 2.00e-02 2.50e+03 pdb=" N7 A F 16 " 0.018 2.00e-02 2.50e+03 pdb=" C5 A F 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 A F 16 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A F 16 " -0.062 2.00e-02 2.50e+03 pdb=" N1 A F 16 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A F 16 " 0.015 2.00e-02 2.50e+03 pdb=" N3 A F 16 " 0.018 2.00e-02 2.50e+03 pdb=" C4 A F 16 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A F 13 " -0.084 2.00e-02 2.50e+03 3.44e-02 3.26e+01 pdb=" N9 A F 13 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A F 13 " 0.025 2.00e-02 2.50e+03 pdb=" N7 A F 13 " 0.016 2.00e-02 2.50e+03 pdb=" C5 A F 13 " 0.010 2.00e-02 2.50e+03 pdb=" C6 A F 13 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A F 13 " -0.053 2.00e-02 2.50e+03 pdb=" N1 A F 13 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A F 13 " 0.012 2.00e-02 2.50e+03 pdb=" N3 A F 13 " 0.024 2.00e-02 2.50e+03 pdb=" C4 A F 13 " 0.020 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1575 2.78 - 3.31: 7535 3.31 - 3.84: 13034 3.84 - 4.37: 14550 4.37 - 4.90: 22602 Nonbonded interactions: 59296 Sorted by model distance: nonbonded pdb=" NH1 ARG D 782 " pdb=" OP1 U E 18 " model vdw 2.248 3.120 nonbonded pdb=" NH1 ARG C 10 " pdb=" OH TYR C 64 " model vdw 2.315 3.120 nonbonded pdb=" NH2 ARG C 28 " pdb=" OD2 ASP C 32 " model vdw 2.340 3.120 nonbonded pdb=" O ASP D 102 " pdb=" OD1 ASP D 102 " model vdw 2.360 3.040 nonbonded pdb=" O GLY D 601 " pdb=" OG1 THR D 604 " model vdw 2.369 3.040 ... (remaining 59291 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' and (resid 695 through 729 or (resid 730 and (name N or name CA or na \ me C or name O or name CB )) or resid 731 through 747)) selection = chain 'B' } 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: 3.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7675 Z= 0.354 Angle : 0.801 8.241 10808 Z= 0.762 Chirality : 0.048 0.198 1333 Planarity : 0.005 0.071 1048 Dihedral : 19.311 130.591 3417 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 19.50 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.23 (0.32), residues: 706 helix: 1.51 (0.25), residues: 430 sheet: -1.66 (0.77), residues: 43 loop : 0.15 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 120 TYR 0.032 0.001 TYR D 670 PHE 0.011 0.001 PHE D 16 TRP 0.003 0.001 TRP D 692 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.35 ( 7675) covalent geometry : angle 0.80066 / 0.76 (10808) hydrogen bonds : bond 0.19442 / 13.18 ( 455) hydrogen bonds : angle 6.97259 / 5.26 ( 1216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 717 LYS cc_start: 0.8011 (tppt) cc_final: 0.7772 (mmmm) REVERT: B 728 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7643 (mm-40) REVERT: B 738 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7636 (tm-30) REVERT: D 602 LEU cc_start: 0.7827 (tp) cc_final: 0.7609 (tp) REVERT: D 730 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6630 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1088 time to fit residues: 16.4565 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 128 GLN D 643 HIS D 647 GLN D 720 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.159492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125472 restraints weight = 14954.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124127 restraints weight = 18053.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126053 restraints weight = 16030.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125529 restraints weight = 11854.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125918 restraints weight = 12186.488| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7675 Z= 0.210 Angle : 0.647 8.783 10808 Z= 0.358 Chirality : 0.041 0.169 1333 Planarity : 0.006 0.063 1048 Dihedral : 18.427 123.536 2222 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.73 % Rotamer: Outliers : 3.47 % Allowed : 18.53 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.33 (0.31), residues: 706 helix: 1.59 (0.24), residues: 441 sheet: -1.80 (0.77), residues: 37 loop : 0.09 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 120 TYR 0.015 0.002 TYR D 789 PHE 0.018 0.002 PHE C 104 TRP 0.005 0.002 TRP D 692 HIS 0.014 0.002 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 ( 7675) covalent geometry : angle 0.64662 / 0.36 (10808) hydrogen bonds : bond 0.06954 / 5.16 ( 455) hydrogen bonds : angle 5.19716 / 3.91 ( 1216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 717 LYS cc_start: 0.8361 (tppt) cc_final: 0.8106 (mmmm) REVERT: B 738 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7048 (tm-30) REVERT: C 163 MET cc_start: 0.6129 (mpp) cc_final: 0.5028 (tmm) REVERT: D 561 ASP cc_start: 0.5360 (OUTLIER) cc_final: 0.4682 (m-30) outliers start: 18 outliers final: 8 residues processed: 116 average time/residue: 0.0966 time to fit residues: 14.6727 Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 618 CYS Chi-restraints excluded: chain D residue 661 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.160549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126145 restraints weight = 14780.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126008 restraints weight = 13764.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126907 restraints weight = 14017.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127466 restraints weight = 9551.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127843 restraints weight = 9226.286| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7675 Z= 0.140 Angle : 0.526 7.396 10808 Z= 0.291 Chirality : 0.036 0.135 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.335 122.055 2222 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.56 % Favored : 98.30 % Rotamer: Outliers : 2.12 % Allowed : 21.04 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.68 (0.32), residues: 706 helix: 1.93 (0.24), residues: 440 sheet: -1.80 (0.74), residues: 37 loop : 0.13 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 94 TYR 0.016 0.001 TYR D 789 PHE 0.026 0.002 PHE C 155 TRP 0.004 0.001 TRP D 692 HIS 0.004 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 7675) covalent geometry : angle 0.52644 / 0.29 (10808) hydrogen bonds : bond 0.05707 / 4.17 ( 455) hydrogen bonds : angle 4.66958 / 3.52 ( 1216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 738 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 163 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5145 (tmm) REVERT: C 164 LEU cc_start: 0.1676 (OUTLIER) cc_final: 0.1124 (mm) REVERT: D 608 HIS cc_start: 0.7658 (t70) cc_final: 0.7431 (t-90) REVERT: D 754 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8256 (mmtp) REVERT: D 811 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6903 (pt0) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 0.1150 time to fit residues: 16.3242 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 661 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.160028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126593 restraints weight = 14877.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126201 restraints weight = 15969.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127042 restraints weight = 17460.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127581 restraints weight = 11435.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127620 restraints weight = 11581.387| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7675 Z= 0.145 Angle : 0.514 7.274 10808 Z= 0.280 Chirality : 0.035 0.138 1333 Planarity : 0.004 0.043 1048 Dihedral : 18.282 122.820 2222 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.84 % Favored : 98.02 % Rotamer: Outliers : 4.05 % Allowed : 21.81 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.32), residues: 706 helix: 2.07 (0.24), residues: 440 sheet: -1.82 (0.76), residues: 37 loop : 0.19 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 799 TYR 0.012 0.001 TYR C 111 PHE 0.011 0.001 PHE C 155 TRP 0.002 0.001 TRP D 692 HIS 0.003 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 7675) covalent geometry : angle 0.51384 / 0.28 (10808) hydrogen bonds : bond 0.05381 / 3.97 ( 455) hydrogen bonds : angle 4.43458 / 3.33 ( 1216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 163 MET cc_start: 0.6053 (mpp) cc_final: 0.5080 (tmm) REVERT: D 109 LEU cc_start: 0.7513 (mt) cc_final: 0.7258 (mp) REVERT: D 561 ASP cc_start: 0.4930 (OUTLIER) cc_final: 0.4300 (m-30) REVERT: D 811 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6846 (pt0) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.1095 time to fit residues: 15.8806 Evaluate side-chains 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.160924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125761 restraints weight = 14996.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125238 restraints weight = 13235.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126424 restraints weight = 13864.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126464 restraints weight = 9819.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126659 restraints weight = 9840.209| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7675 Z= 0.115 Angle : 0.473 7.429 10808 Z= 0.259 Chirality : 0.033 0.136 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.264 127.524 2222 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 3.09 % Allowed : 22.78 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.08 (0.32), residues: 706 helix: 2.27 (0.25), residues: 443 sheet: -1.76 (0.77), residues: 37 loop : 0.21 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 94 TYR 0.016 0.001 TYR D 789 PHE 0.018 0.001 PHE D 629 TRP 0.001 0.000 TRP D 692 HIS 0.002 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 7675) covalent geometry : angle 0.47315 / 0.26 (10808) hydrogen bonds : bond 0.04805 / 3.52 ( 455) hydrogen bonds : angle 4.21603 / 3.16 ( 1216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 67 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7590 (mt) REVERT: C 163 MET cc_start: 0.5807 (mpp) cc_final: 0.5074 (tmm) REVERT: D 109 LEU cc_start: 0.7438 (mt) cc_final: 0.7147 (mp) REVERT: D 811 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6856 (pt0) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1028 time to fit residues: 15.2575 Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 661 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 50.0000 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.161876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126217 restraints weight = 14972.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126520 restraints weight = 12937.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127393 restraints weight = 12528.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127554 restraints weight = 8463.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128102 restraints weight = 8292.627| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7675 Z= 0.132 Angle : 0.494 7.528 10808 Z= 0.265 Chirality : 0.034 0.134 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.253 128.552 2222 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 3.09 % Allowed : 23.17 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.04 (0.32), residues: 706 helix: 2.26 (0.25), residues: 443 sheet: -1.69 (0.79), residues: 37 loop : 0.11 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.013 0.001 TYR D 789 PHE 0.017 0.002 PHE D 629 TRP 0.002 0.000 TRP D 692 HIS 0.003 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7675) covalent geometry : angle 0.49446 / 0.27 (10808) hydrogen bonds : bond 0.04860 / 3.58 ( 455) hydrogen bonds : angle 4.16745 / 3.12 ( 1216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 67 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7599 (mt) REVERT: D 109 LEU cc_start: 0.7536 (mt) cc_final: 0.7209 (mp) REVERT: D 730 ARG cc_start: 0.6136 (mtp180) cc_final: 0.5894 (mmm-85) REVERT: D 811 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6857 (pt0) outliers start: 16 outliers final: 13 residues processed: 106 average time/residue: 0.0941 time to fit residues: 13.2564 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 733 PHE Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.161122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125103 restraints weight = 15026.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125359 restraints weight = 12386.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126224 restraints weight = 12090.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126394 restraints weight = 8252.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126578 restraints weight = 8266.021| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7675 Z= 0.141 Angle : 0.492 7.971 10808 Z= 0.265 Chirality : 0.034 0.136 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.255 128.250 2222 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 3.67 % Allowed : 23.17 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.98 (0.32), residues: 706 helix: 2.23 (0.25), residues: 442 sheet: -1.69 (0.79), residues: 37 loop : 0.08 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.010 0.001 TYR D 670 PHE 0.018 0.002 PHE D 629 TRP 0.002 0.001 TRP D 692 HIS 0.002 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 7675) covalent geometry : angle 0.49239 / 0.27 (10808) hydrogen bonds : bond 0.04831 / 3.56 ( 455) hydrogen bonds : angle 4.14196 / 3.10 ( 1216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 67 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7578 (mt) REVERT: D 109 LEU cc_start: 0.7519 (mt) cc_final: 0.7181 (mp) REVERT: D 561 ASP cc_start: 0.5101 (OUTLIER) cc_final: 0.4518 (m-30) REVERT: D 730 ARG cc_start: 0.6226 (mtp180) cc_final: 0.5946 (mmm-85) REVERT: D 811 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6834 (pt0) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.1039 time to fit residues: 14.2684 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 733 PHE Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123337 restraints weight = 15154.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123376 restraints weight = 12705.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124288 restraints weight = 11534.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125157 restraints weight = 8295.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125341 restraints weight = 7678.296| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7675 Z= 0.173 Angle : 0.529 8.073 10808 Z= 0.283 Chirality : 0.036 0.140 1333 Planarity : 0.004 0.043 1048 Dihedral : 18.305 128.724 2222 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.55 % Favored : 97.31 % Rotamer: Outliers : 2.90 % Allowed : 24.13 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.65 (0.32), residues: 706 helix: 2.04 (0.24), residues: 448 sheet: -1.74 (0.87), residues: 32 loop : -0.35 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 94 TYR 0.009 0.001 TYR D 670 PHE 0.011 0.002 PHE C 60 TRP 0.006 0.001 TRP D 692 HIS 0.004 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 7675) covalent geometry : angle 0.52856 / 0.28 (10808) hydrogen bonds : bond 0.05215 / 3.87 ( 455) hydrogen bonds : angle 4.20759 / 3.15 ( 1216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7641 (ttm-80) REVERT: B 725 LEU cc_start: 0.9281 (tp) cc_final: 0.9015 (tt) REVERT: B 735 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7704 (tm-30) REVERT: C 67 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7633 (mt) REVERT: D 109 LEU cc_start: 0.7755 (mt) cc_final: 0.7370 (mp) REVERT: D 701 MET cc_start: 0.2330 (mtp) cc_final: 0.2093 (mtp) REVERT: D 730 ARG cc_start: 0.6257 (mtp180) cc_final: 0.5851 (mmm-85) REVERT: D 811 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6825 (pt0) outliers start: 15 outliers final: 13 residues processed: 102 average time/residue: 0.1005 time to fit residues: 13.6575 Evaluate side-chains 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 733 PHE Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 50.0000 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125508 restraints weight = 14913.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125700 restraints weight = 12208.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126719 restraints weight = 11182.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126853 restraints weight = 7939.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.127140 restraints weight = 7716.573| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7675 Z= 0.121 Angle : 0.501 9.471 10808 Z= 0.266 Chirality : 0.033 0.140 1333 Planarity : 0.004 0.047 1048 Dihedral : 18.287 128.965 2222 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 2.70 % Allowed : 24.71 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.86 (0.32), residues: 706 helix: 2.18 (0.24), residues: 449 sheet: -1.74 (0.85), residues: 32 loop : -0.21 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 634 TYR 0.008 0.001 TYR D 103 PHE 0.009 0.001 PHE D 629 TRP 0.001 0.000 TRP D 692 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7675) covalent geometry : angle 0.50134 / 0.27 (10808) hydrogen bonds : bond 0.04612 / 3.38 ( 455) hydrogen bonds : angle 4.07456 / 3.05 ( 1216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7581 (ttm-80) REVERT: B 735 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 67 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7648 (mt) REVERT: D 109 LEU cc_start: 0.7519 (mt) cc_final: 0.7164 (mp) REVERT: D 701 MET cc_start: 0.2012 (mtp) cc_final: 0.1715 (mtp) REVERT: D 730 ARG cc_start: 0.6178 (mtp180) cc_final: 0.5688 (mmm-85) REVERT: D 811 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6876 (pt0) outliers start: 14 outliers final: 11 residues processed: 105 average time/residue: 0.0960 time to fit residues: 13.3310 Evaluate side-chains 104 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 0.0020 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.162225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.126154 restraints weight = 15005.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126327 restraints weight = 11843.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127396 restraints weight = 10752.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127519 restraints weight = 7680.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127827 restraints weight = 7446.825| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7675 Z= 0.111 Angle : 0.484 8.293 10808 Z= 0.259 Chirality : 0.033 0.138 1333 Planarity : 0.005 0.134 1048 Dihedral : 18.261 128.532 2222 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.73 % Rotamer: Outliers : 2.32 % Allowed : 25.29 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.93 (0.33), residues: 706 helix: 2.22 (0.25), residues: 450 sheet: -1.69 (0.86), residues: 32 loop : -0.16 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 634 TYR 0.007 0.001 TYR D 626 PHE 0.008 0.001 PHE C 60 TRP 0.001 0.000 TRP D 692 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7675) covalent geometry : angle 0.48387 / 0.26 (10808) hydrogen bonds : bond 0.04399 / 3.20 ( 455) hydrogen bonds : angle 3.98487 / 2.98 ( 1216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 736 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7547 (ttm-80) REVERT: B 735 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 67 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7635 (mt) REVERT: D 109 LEU cc_start: 0.7453 (mt) cc_final: 0.7084 (mp) REVERT: D 730 ARG cc_start: 0.6161 (mtp180) cc_final: 0.5905 (mmm-85) REVERT: D 811 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6874 (pt0) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.0956 time to fit residues: 13.1210 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 120 ARG Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.162149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126186 restraints weight = 14952.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125932 restraints weight = 12090.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126895 restraints weight = 11337.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127489 restraints weight = 8110.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127700 restraints weight = 7793.737| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7675 Z= 0.122 Angle : 0.499 10.733 10808 Z= 0.262 Chirality : 0.033 0.140 1333 Planarity : 0.005 0.096 1048 Dihedral : 18.255 128.001 2222 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 2.51 % Allowed : 24.71 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.95 (0.33), residues: 706 helix: 2.22 (0.24), residues: 449 sheet: -1.64 (0.87), residues: 32 loop : -0.12 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 634 TYR 0.007 0.001 TYR D 685 PHE 0.010 0.001 PHE D 629 TRP 0.002 0.001 TRP D 692 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7675) covalent geometry : angle 0.49916 / 0.26 (10808) hydrogen bonds : bond 0.04432 / 3.24 ( 455) hydrogen bonds : angle 3.96330 / 2.96 ( 1216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.94 seconds wall clock time: 22 minutes 57.36 seconds (1377.36 seconds total)