Starting phenix.real_space_refine on Thu Jul 2 07:21:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwa_54305/07_2026/9rwa_54305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwa_54305/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rwa_54305/07_2026/9rwa_54305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwa_54305/07_2026/9rwa_54305.map" model { file = "/net/cci-nas-00/data/ceres_data/9rwa_54305/07_2026/9rwa_54305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwa_54305/07_2026/9rwa_54305.cif" } 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): 0.01s 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: 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: 1.44, per 1000 atoms: 0.20 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: 0.51 Conformation dependent library (CDL) restraints added in 210.5 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: 0.76 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: 1.34 Time building geometry restraints manager: 0.69 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: 10323 1.65 - 3.30: 434 3.30 - 4.94: 40 4.94 - 6.59: 9 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 1.50e+00 4.44e-01 3.02e+01 angle pdb=" N6 A F 49 " pdb=" C6 A F 49 " pdb=" N1 A F 49 " ideal model delta sigma weight residual 118.60 115.55 3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" N6 A F 31 " pdb=" C6 A F 31 " pdb=" N1 A F 31 " ideal model delta sigma weight residual 118.60 115.59 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" C5 G F 7 " pdb=" C6 G F 7 " pdb=" N1 G F 7 " ideal model delta sigma weight residual 111.50 114.00 -2.50 5.00e-01 4.00e+00 2.50e+01 angle pdb=" O6 G F 32 " pdb=" C6 G F 32 " pdb=" N1 G F 32 " ideal model delta sigma weight residual 119.90 116.92 2.98 6.00e-01 2.78e+00 2.46e+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: 1033 0.040 - 0.079: 202 0.079 - 0.119: 85 0.119 - 0.158: 11 0.158 - 0.198: 2 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=" C1' G F 43 " pdb=" O4' G F 43 " pdb=" C2' G F 43 " pdb=" N9 G F 43 " both_signs ideal model delta sigma weight residual False 2.46 2.61 -0.16 2.00e-01 2.50e+01 6.08e-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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- 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= 0.330 Angle : 0.729 8.241 10808 Z= 0.670 Chirality : 0.039 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 0.00383 / 0.33 ( 7675) covalent geometry : angle 0.72893 / 0.67 (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 : 0.197 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: 0.7634 (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: 0.6629 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0935 time to fit residues: 14.1852 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 643 HIS D 647 GLN D 720 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.159478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125214 restraints weight = 14969.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124078 restraints weight = 17049.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125709 restraints weight = 15749.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125246 restraints weight = 11871.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.125655 restraints weight = 11148.887| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7675 Z= 0.205 Angle : 0.629 8.225 10808 Z= 0.350 Chirality : 0.041 0.201 1333 Planarity : 0.006 0.058 1048 Dihedral : 18.372 125.125 2222 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.12 % Favored : 97.73 % Rotamer: Outliers : 3.28 % Allowed : 18.73 % 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: 1.31 (0.31), residues: 706 helix: 1.58 (0.24), residues: 441 sheet: -1.83 (0.77), residues: 37 loop : 0.10 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 120 TYR 0.015 0.002 TYR C 103 PHE 0.018 0.002 PHE C 104 TRP 0.004 0.002 TRP D 692 HIS 0.013 0.002 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 ( 7675) covalent geometry : angle 0.62898 / 0.35 (10808) hydrogen bonds : bond 0.06624 / 4.89 ( 455) hydrogen bonds : angle 5.17936 / 3.90 ( 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: 17 poor density : 104 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 717 LYS cc_start: 0.8363 (tppt) cc_final: 0.8008 (mtpp) REVERT: B 738 GLU cc_start: 0.7314 (tm-30) cc_final: 0.7035 (tm-30) REVERT: C 163 MET cc_start: 0.6216 (mpp) cc_final: 0.5080 (tmm) REVERT: D 561 ASP cc_start: 0.5351 (OUTLIER) cc_final: 0.4677 (m-30) outliers start: 17 outliers final: 8 residues processed: 116 average time/residue: 0.0841 time to fit residues: 12.7384 Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 52 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.160020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126732 restraints weight = 14700.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.124870 restraints weight = 19323.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125669 restraints weight = 18341.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126626 restraints weight = 13300.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126811 restraints weight = 11688.294| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7675 Z= 0.148 Angle : 0.523 6.835 10808 Z= 0.291 Chirality : 0.036 0.165 1333 Planarity : 0.004 0.043 1048 Dihedral : 18.313 125.140 2222 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 2.51 % Allowed : 20.46 % Favored : 77.03 % 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: 1.64 (0.32), residues: 706 helix: 1.90 (0.24), residues: 439 sheet: -1.87 (0.74), residues: 37 loop : 0.12 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 126 TYR 0.015 0.001 TYR D 789 PHE 0.022 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 0.00317 / 0.15 ( 7675) covalent geometry : angle 0.52301 / 0.29 (10808) hydrogen bonds : bond 0.05479 / 4.01 ( 455) hydrogen bonds : angle 4.67691 / 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 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 738 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7135 (tm-30) REVERT: C 163 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5129 (tmm) REVERT: C 164 LEU cc_start: 0.1678 (OUTLIER) cc_final: 0.1134 (mm) REVERT: D 754 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8174 (mmtp) REVERT: D 811 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6902 (pt0) outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 0.0910 time to fit residues: 13.1334 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 C residue 148 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: 0.0980 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.160311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126621 restraints weight = 14774.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.126231 restraints weight = 15093.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127951 restraints weight = 14256.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127412 restraints weight = 10716.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128183 restraints weight = 11389.437| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7675 Z= 0.131 Angle : 0.493 6.828 10808 Z= 0.272 Chirality : 0.035 0.139 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.250 125.945 2222 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.84 % Favored : 98.02 % Rotamer: Outliers : 3.86 % Allowed : 21.43 % Favored : 74.71 % 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: 1.88 (0.32), residues: 706 helix: 2.10 (0.24), residues: 440 sheet: -1.86 (0.75), residues: 37 loop : 0.20 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 94 TYR 0.012 0.001 TYR C 111 PHE 0.010 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 0.00281 / 0.13 ( 7675) covalent geometry : angle 0.49326 / 0.27 (10808) hydrogen bonds : bond 0.05012 / 3.66 ( 455) hydrogen bonds : angle 4.33273 / 3.24 ( 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 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7614 (mt) REVERT: C 163 MET cc_start: 0.6088 (mpp) cc_final: 0.5109 (tmm) REVERT: D 796 GLU cc_start: 0.6380 (mt-10) cc_final: 0.5478 (mm-30) REVERT: D 811 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6841 (pt0) outliers start: 20 outliers final: 15 residues processed: 118 average time/residue: 0.0818 time to fit residues: 12.4648 Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 142 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 165 VAL 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: 6.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.160300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126185 restraints weight = 14827.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127195 restraints weight = 12496.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127757 restraints weight = 12827.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127646 restraints weight = 8768.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127849 restraints weight = 9027.845| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2712 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= 0.124 Angle : 0.481 7.277 10808 Z= 0.263 Chirality : 0.034 0.134 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.256 130.079 2222 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 2.90 % Allowed : 22.59 % Favored : 74.52 % 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: 2.03 (0.32), residues: 706 helix: 2.25 (0.25), residues: 441 sheet: -1.84 (0.76), residues: 37 loop : 0.20 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 736 TYR 0.013 0.001 TYR D 789 PHE 0.008 0.001 PHE C 60 TRP 0.001 0.000 TRP D 692 HIS 0.006 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7675) covalent geometry : angle 0.48121 / 0.26 (10808) hydrogen bonds : bond 0.04722 / 3.47 ( 455) hydrogen bonds : angle 4.19951 / 3.14 ( 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7788 (tm-30) REVERT: C 67 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7581 (mt) REVERT: C 163 MET cc_start: 0.5970 (mpp) cc_final: 0.5091 (tmm) REVERT: D 730 ARG cc_start: 0.6055 (mtp180) cc_final: 0.5826 (mmm-85) REVERT: D 811 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6841 (pt0) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.0793 time to fit residues: 11.4154 Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 602 LEU 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: 0.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.162276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126844 restraints weight = 14964.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.126902 restraints weight = 12676.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.127959 restraints weight = 12514.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.127985 restraints weight = 8599.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128323 restraints weight = 8724.036| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2827 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= 0.121 Angle : 0.471 7.484 10808 Z= 0.257 Chirality : 0.034 0.149 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.249 131.649 2222 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 3.09 % Allowed : 22.20 % Favored : 74.71 % 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: 2.05 (0.33), residues: 706 helix: 2.26 (0.25), residues: 442 sheet: -1.77 (0.77), residues: 37 loop : 0.18 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 94 TYR 0.013 0.001 TYR D 789 PHE 0.018 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 0.47114 / 0.26 (10808) hydrogen bonds : bond 0.04551 / 3.34 ( 455) hydrogen bonds : angle 4.11095 / 3.07 ( 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 : 0.150 Fit side-chains revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 67 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7622 (mt) REVERT: C 163 MET cc_start: 0.5841 (mpp) cc_final: 0.5112 (tmm) REVERT: D 811 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6848 (pt0) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.0703 time to fit residues: 9.8589 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 725 LEU 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 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 Chi-restraints excluded: chain D residue 661 ILE 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: 1.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.159587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123345 restraints weight = 14994.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123684 restraints weight = 12253.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124643 restraints weight = 11311.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124685 restraints weight = 7993.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125057 restraints weight = 7889.870| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7675 Z= 0.185 Angle : 0.541 7.984 10808 Z= 0.292 Chirality : 0.036 0.148 1333 Planarity : 0.004 0.049 1048 Dihedral : 18.289 131.520 2222 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 4.44 % Allowed : 21.62 % Favored : 73.94 % 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: 1.78 (0.32), residues: 706 helix: 2.07 (0.24), residues: 442 sheet: -1.76 (0.79), residues: 37 loop : -0.01 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 120 TYR 0.011 0.002 TYR D 626 PHE 0.017 0.002 PHE D 629 TRP 0.005 0.001 TRP D 692 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 7675) covalent geometry : angle 0.54106 / 0.29 (10808) hydrogen bonds : bond 0.05182 / 3.85 ( 455) hydrogen bonds : angle 4.24252 / 3.18 ( 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 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 725 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8968 (tt) REVERT: B 735 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 109 LEU cc_start: 0.7562 (mt) cc_final: 0.7330 (mp) REVERT: D 561 ASP cc_start: 0.5229 (OUTLIER) cc_final: 0.4436 (m-30) REVERT: D 663 LEU cc_start: 0.6723 (tp) cc_final: 0.6506 (tp) REVERT: D 811 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6832 (pt0) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.0694 time to fit residues: 10.0665 Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 725 LEU 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 77 VAL 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 163 MET Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 561 ASP Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 800 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.160835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124665 restraints weight = 15209.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124770 restraints weight = 12158.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125792 restraints weight = 11503.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126022 restraints weight = 8218.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126377 restraints weight = 7950.377| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7675 Z= 0.141 Angle : 0.507 8.050 10808 Z= 0.271 Chirality : 0.035 0.154 1333 Planarity : 0.004 0.043 1048 Dihedral : 18.275 131.721 2222 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 2.90 % Allowed : 23.55 % Favored : 73.55 % 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: 1.91 (0.32), residues: 706 helix: 2.16 (0.24), residues: 442 sheet: -1.64 (0.84), residues: 32 loop : 0.01 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 120 TYR 0.015 0.001 TYR D 626 PHE 0.016 0.002 PHE D 629 TRP 0.002 0.001 TRP D 692 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7675) covalent geometry : angle 0.50708 / 0.27 (10808) hydrogen bonds : bond 0.04639 / 3.42 ( 455) hydrogen bonds : angle 4.14435 / 3.10 ( 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 106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 735 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7720 (tm-30) REVERT: D 109 LEU cc_start: 0.7452 (mt) cc_final: 0.7215 (mp) REVERT: D 561 ASP cc_start: 0.5052 (OUTLIER) cc_final: 0.4550 (m-30) REVERT: D 663 LEU cc_start: 0.6716 (tp) cc_final: 0.6502 (tp) REVERT: D 811 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6827 (pt0) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.0839 time to fit residues: 10.7485 Evaluate side-chains 102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 725 LEU 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 77 VAL 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 561 ASP 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: 0.7980 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 0.0270 chunk 17 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.161958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126644 restraints weight = 14892.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.124304 restraints weight = 13526.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125784 restraints weight = 10930.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126609 restraints weight = 8676.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126385 restraints weight = 8332.933| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3214 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= 0.115 Angle : 0.481 8.287 10808 Z= 0.258 Chirality : 0.033 0.154 1333 Planarity : 0.003 0.042 1048 Dihedral : 18.242 131.661 2222 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 3.28 % Allowed : 23.17 % Favored : 73.55 % 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: 2.05 (0.33), residues: 706 helix: 2.27 (0.25), residues: 443 sheet: -1.71 (0.81), residues: 32 loop : 0.10 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 120 TYR 0.014 0.001 TYR D 626 PHE 0.016 0.001 PHE D 629 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 0.00248 / 0.11 ( 7675) covalent geometry : angle 0.48076 / 0.26 (10808) hydrogen bonds : bond 0.04299 / 3.14 ( 455) hydrogen bonds : angle 4.01702 / 2.99 ( 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 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 725 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8869 (tt) REVERT: B 735 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7792 (tm-30) REVERT: D 8 MET cc_start: 0.8269 (tpp) cc_final: 0.8017 (tpp) REVERT: D 109 LEU cc_start: 0.7404 (mt) cc_final: 0.7175 (mp) REVERT: D 730 ARG cc_start: 0.6017 (mtp180) cc_final: 0.5729 (mtp180) REVERT: D 811 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6901 (pt0) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.0765 time to fit residues: 10.1672 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU 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 C residue 163 MET Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 616 HIS Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 800 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 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: 3.9990 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.161802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126754 restraints weight = 15020.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125050 restraints weight = 12370.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125975 restraints weight = 11492.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126771 restraints weight = 8555.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126892 restraints weight = 7886.758| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3310 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 : 0.484 8.678 10808 Z= 0.257 Chirality : 0.033 0.163 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.221 131.146 2222 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % Rotamer: Outliers : 2.90 % Allowed : 23.55 % Favored : 73.55 % 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: 2.11 (0.33), residues: 706 helix: 2.29 (0.25), residues: 443 sheet: -1.61 (0.76), residues: 37 loop : 0.21 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 120 TYR 0.012 0.001 TYR D 626 PHE 0.019 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 0.48360 / 0.26 (10808) hydrogen bonds : bond 0.04299 / 3.15 ( 455) hydrogen bonds : angle 3.98000 / 2.97 ( 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 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 725 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8873 (tt) REVERT: B 735 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 8 MET cc_start: 0.8275 (tpp) cc_final: 0.8044 (tpp) REVERT: D 109 LEU cc_start: 0.7401 (mt) cc_final: 0.7173 (mp) REVERT: D 730 ARG cc_start: 0.5988 (mtp180) cc_final: 0.5685 (mtp180) REVERT: D 811 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6890 (pt0) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.0703 time to fit residues: 9.5547 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 739 GLU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 15 LEU 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 C residue 163 MET 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 Chi-restraints excluded: chain D residue 800 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.161610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126326 restraints weight = 14879.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125081 restraints weight = 12389.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126425 restraints weight = 11305.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126756 restraints weight = 8305.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126745 restraints weight = 8446.751| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3391 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= 0.127 Angle : 0.491 9.784 10808 Z= 0.261 Chirality : 0.034 0.170 1333 Planarity : 0.004 0.042 1048 Dihedral : 18.226 130.567 2222 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.98 % Favored : 97.88 % 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: 2.13 (0.33), residues: 706 helix: 2.29 (0.24), residues: 443 sheet: -1.51 (0.83), residues: 32 loop : 0.19 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 120 TYR 0.011 0.001 TYR D 626 PHE 0.019 0.002 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 0.00278 / 0.13 ( 7675) covalent geometry : angle 0.49142 / 0.26 (10808) hydrogen bonds : bond 0.04327 / 3.17 ( 455) hydrogen bonds : angle 3.97111 / 2.96 ( 1216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.89 seconds wall clock time: 18 minutes 54.22 seconds (1134.22 seconds total)