Starting phenix.real_space_refine on Fri Jun 13 20:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8m_61231/06_2025/9j8m_61231.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 368 5.49 5 S 27 5.16 5 C 8796 2.51 5 N 2945 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3753 Classifications: {'DNA': 184} Link IDs: {'rna3p': 183} Chain: "J" Number of atoms: 3791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3791 Classifications: {'DNA': 184} Link IDs: {'rna3p': 183} Chain: "K" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "L" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG M 453 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG M 453 " occ=0.50 Time building chain proxies: 8.77, per 1000 atoms: 0.55 Number of scatterers: 15831 At special positions: 0 Unit cell: (167.48, 117.66, 145.22, 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 368 15.00 O 3695 8.00 N 2945 7.00 C 8796 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: 3.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 66.7% alpha, 6.9% beta 184 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.531A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.686A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.581A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.501A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.504A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.620A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.569A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.009A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.911A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.605A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.728A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 4 through 13 removed outlier: 3.950A pdb=" N GLU K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 52 Processing helix chain 'K' and resid 55 through 68 Processing helix chain 'K' and resid 70 through 88 Processing helix chain 'L' and resid 4 through 13 removed outlier: 4.030A pdb=" N GLU L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 38 Processing helix chain 'L' and resid 41 through 52 Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'L' and resid 70 through 89 Processing helix chain 'M' and resid 501 through 503 No H-bonds generated for 'chain 'M' and resid 501 through 503' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.558A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.373A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.384A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.349A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 8.000A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 430 through 436 removed outlier: 3.530A pdb=" N ALA M 539 " --> pdb=" O LEU M 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 440 through 445 removed outlier: 5.520A pdb=" N VAL M 442 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG M 455 " --> pdb=" O VAL M 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 462 through 463 529 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 473 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3182 1.33 - 1.45: 5359 1.45 - 1.57: 7558 1.57 - 1.69: 734 1.69 - 1.81: 41 Bond restraints: 16874 Sorted by residual: bond pdb=" O3' DG J 102 " pdb=" P DT J 103 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.50e-02 4.44e+03 9.37e+00 bond pdb=" N ASN M 466 " pdb=" CA ASN M 466 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.39e-02 5.18e+03 5.47e+00 bond pdb=" O3' DC J 99 " pdb=" P DG J 100 " ideal model delta sigma weight residual 1.607 1.640 -0.033 1.50e-02 4.44e+03 4.71e+00 bond pdb=" C3' DT J 152 " pdb=" O3' DT J 152 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.32e+00 ... (remaining 16869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 23533 1.30 - 2.59: 782 2.59 - 3.89: 38 3.89 - 5.18: 7 5.18 - 6.48: 3 Bond angle restraints: 24363 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.43 109.23 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 110.77 117.25 -6.48 1.93e+00 2.68e-01 1.13e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 116.79 -5.77 1.86e+00 2.89e-01 9.63e+00 angle pdb=" N LYS G 74 " pdb=" CA LYS G 74 " pdb=" CB LYS G 74 " ideal model delta sigma weight residual 113.65 110.10 3.55 1.47e+00 4.63e-01 5.84e+00 angle pdb=" CA ASN M 466 " pdb=" C ASN M 466 " pdb=" O ASN M 466 " ideal model delta sigma weight residual 120.32 117.72 2.60 1.18e+00 7.18e-01 4.87e+00 ... (remaining 24358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 7534 35.45 - 70.90: 1601 70.90 - 106.35: 17 106.35 - 141.80: 0 141.80 - 177.25: 2 Dihedral angle restraints: 9154 sinusoidal: 6151 harmonic: 3003 Sorted by residual: dihedral pdb=" C4' DT J 152 " pdb=" C3' DT J 152 " pdb=" O3' DT J 152 " pdb=" P DC J 153 " ideal model delta sinusoidal sigma weight residual 220.00 42.75 177.25 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 118 " pdb=" C3' DG J 118 " pdb=" O3' DG J 118 " pdb=" P DG J 119 " ideal model delta sinusoidal sigma weight residual 220.00 75.54 144.46 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" N LEU A 65 " pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sinusoidal sigma weight residual -60.00 -118.92 58.92 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1722 0.026 - 0.053: 777 0.053 - 0.079: 165 0.079 - 0.105: 57 0.105 - 0.131: 21 Chirality restraints: 2742 Sorted by residual: chirality pdb=" P DG J 100 " pdb=" OP1 DG J 100 " pdb=" OP2 DG J 100 " pdb=" O5' DG J 100 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ASN M 466 " pdb=" N ASN M 466 " pdb=" C ASN M 466 " pdb=" CB ASN M 466 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 2739 not shown) Planarity restraints: 1819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 113 " -0.024 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" N9 DA I 113 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 113 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 113 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 113 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 113 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 113 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 113 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 113 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 113 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 113 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 42 " -0.021 2.00e-02 2.50e+03 9.50e-03 2.48e+00 pdb=" N9 DA I 42 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 42 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 42 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 42 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 42 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 42 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 42 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 42 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 42 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 42 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 41 " -0.019 2.00e-02 2.50e+03 8.18e-03 2.01e+00 pdb=" N9 DG I 41 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 41 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 41 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 41 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 41 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 41 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 41 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 41 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 41 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 41 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 41 " -0.001 2.00e-02 2.50e+03 ... (remaining 1816 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2979 2.79 - 3.32: 14177 3.32 - 3.85: 30836 3.85 - 4.37: 34903 4.37 - 4.90: 50618 Nonbonded interactions: 133513 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.264 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.282 3.040 nonbonded pdb=" NH2 ARG G 20 " pdb=" OP1 DT I 54 " model vdw 2.317 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.328 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.328 3.040 ... (remaining 133508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.50 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: 0.840 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.580 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16874 Z= 0.149 Angle : 0.521 6.479 24363 Z= 0.328 Chirality : 0.032 0.131 2742 Planarity : 0.003 0.031 1819 Dihedral : 26.318 177.245 7220 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.49 % Allowed : 3.79 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.26), residues: 1025 helix: 2.81 (0.20), residues: 657 sheet: 2.21 (0.79), residues: 50 loop : 0.22 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 498 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE L 49 TYR 0.012 0.001 TYR G 57 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.10776 ( 1002) hydrogen bonds : angle 4.22333 ( 2493) covalent geometry : bond 0.00294 (16874) covalent geometry : angle 0.52122 (24363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 42 TYR cc_start: 0.7640 (t80) cc_final: 0.7381 (t80) REVERT: L 6 LYS cc_start: 0.6747 (tttm) cc_final: 0.6040 (mtmm) outliers start: 13 outliers final: 6 residues processed: 218 average time/residue: 0.3850 time to fit residues: 112.2665 Evaluate side-chains 101 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain K residue 80 CYS Chi-restraints excluded: chain L residue 32 LYS Chi-restraints excluded: chain L residue 80 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN D 49 HIS E 39 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN G 112 GLN H 95 GLN L 5 GLN L 7 HIS L 48 GLN ** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.053327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036434 restraints weight = 127446.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.037212 restraints weight = 61769.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037708 restraints weight = 40410.991| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16874 Z= 0.226 Angle : 0.598 7.445 24363 Z= 0.352 Chirality : 0.035 0.152 2742 Planarity : 0.004 0.052 1819 Dihedral : 30.044 179.927 5176 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.18 % Allowed : 10.79 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.26), residues: 1025 helix: 2.63 (0.20), residues: 667 sheet: 1.60 (0.80), residues: 50 loop : 0.15 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 498 HIS 0.007 0.001 HIS F 75 PHE 0.021 0.002 PHE L 59 TYR 0.019 0.002 TYR F 88 ARG 0.008 0.001 ARG K 82 Details of bonding type rmsd hydrogen bonds : bond 0.05174 ( 1002) hydrogen bonds : angle 3.53835 ( 2493) covalent geometry : bond 0.00498 (16874) covalent geometry : angle 0.59813 (24363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7639 (mtt) cc_final: 0.7296 (mtt) REVERT: B 84 MET cc_start: 0.8809 (mmm) cc_final: 0.8298 (mmm) REVERT: C 91 GLU cc_start: 0.8668 (tp30) cc_final: 0.8255 (tp30) REVERT: H 42 TYR cc_start: 0.8034 (t80) cc_final: 0.7805 (t80) REVERT: K 10 PHE cc_start: 0.7065 (t80) cc_final: 0.6655 (t80) REVERT: K 48 GLN cc_start: 0.8125 (mp10) cc_final: 0.7868 (mp10) REVERT: K 82 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8310 (tpm170) REVERT: L 6 LYS cc_start: 0.8692 (tttm) cc_final: 0.7972 (pttm) REVERT: M 447 GLU cc_start: 0.8482 (mp0) cc_final: 0.7843 (mt-10) REVERT: M 453 ARG cc_start: 0.8960 (ttm170) cc_final: 0.8687 (ttm110) REVERT: M 470 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8119 (mmtm) REVERT: M 481 TYR cc_start: 0.8076 (t80) cc_final: 0.7815 (t80) outliers start: 19 outliers final: 9 residues processed: 123 average time/residue: 0.2805 time to fit residues: 50.4767 Evaluate side-chains 99 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 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 = 0.3570 r_free = 0.3570 target = 0.053081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036125 restraints weight = 126083.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.036937 restraints weight = 60983.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037444 restraints weight = 40110.980| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16874 Z= 0.201 Angle : 0.572 6.618 24363 Z= 0.337 Chirality : 0.034 0.149 2742 Planarity : 0.004 0.052 1819 Dihedral : 30.113 179.395 5168 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.41 % Allowed : 10.79 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.26), residues: 1025 helix: 2.63 (0.20), residues: 668 sheet: 1.57 (0.80), residues: 49 loop : 0.14 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 498 HIS 0.004 0.001 HIS E 113 PHE 0.021 0.001 PHE L 59 TYR 0.013 0.002 TYR B 51 ARG 0.003 0.000 ARG M 482 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 1002) hydrogen bonds : angle 3.38143 ( 2493) covalent geometry : bond 0.00441 (16874) covalent geometry : angle 0.57222 (24363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8775 (mmm) cc_final: 0.8330 (mmm) REVERT: C 91 GLU cc_start: 0.8614 (tp30) cc_final: 0.8253 (tp30) REVERT: E 97 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7138 (mt-10) REVERT: H 42 TYR cc_start: 0.7937 (t80) cc_final: 0.7718 (t80) REVERT: K 10 PHE cc_start: 0.7055 (t80) cc_final: 0.6659 (t80) REVERT: K 57 ASP cc_start: 0.9301 (t70) cc_final: 0.9090 (t70) REVERT: L 6 LYS cc_start: 0.8773 (tttm) cc_final: 0.8134 (pttm) REVERT: M 447 GLU cc_start: 0.8433 (mp0) cc_final: 0.7837 (mt-10) REVERT: M 470 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7932 (mmtm) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 0.2951 time to fit residues: 49.8951 Evaluate side-chains 98 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain K residue 39 PHE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 121 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.053439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.036413 restraints weight = 125668.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.037241 restraints weight = 60402.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.037741 restraints weight = 39607.378| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16874 Z= 0.157 Angle : 0.549 7.138 24363 Z= 0.325 Chirality : 0.033 0.145 2742 Planarity : 0.003 0.043 1819 Dihedral : 29.950 178.849 5168 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.95 % Allowed : 13.32 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.27), residues: 1025 helix: 2.81 (0.20), residues: 669 sheet: 1.14 (0.79), residues: 50 loop : 0.27 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 514 HIS 0.004 0.001 HIS A 113 PHE 0.016 0.001 PHE L 59 TYR 0.014 0.001 TYR M 481 ARG 0.006 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1002) hydrogen bonds : angle 3.15310 ( 2493) covalent geometry : bond 0.00336 (16874) covalent geometry : angle 0.54853 (24363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8832 (mmm) cc_final: 0.8448 (mmm) REVERT: C 91 GLU cc_start: 0.8540 (tp30) cc_final: 0.8318 (tp30) REVERT: H 42 TYR cc_start: 0.7824 (t80) cc_final: 0.7554 (t80) REVERT: K 10 PHE cc_start: 0.6914 (t80) cc_final: 0.6570 (t80) REVERT: K 82 ARG cc_start: 0.8998 (tmm-80) cc_final: 0.8423 (tpm170) REVERT: L 6 LYS cc_start: 0.8820 (tttm) cc_final: 0.8207 (ptpp) REVERT: M 447 GLU cc_start: 0.8334 (mp0) cc_final: 0.7694 (mt-10) REVERT: M 470 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7876 (mmtm) REVERT: M 531 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8722 (mm) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.2901 time to fit residues: 49.9430 Evaluate side-chains 103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain M residue 531 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.053243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.036325 restraints weight = 127973.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.037124 restraints weight = 61773.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037631 restraints weight = 40431.210| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.035 16874 Z= 0.188 Angle : 0.573 9.300 24363 Z= 0.335 Chirality : 0.033 0.212 2742 Planarity : 0.004 0.041 1819 Dihedral : 30.019 178.546 5167 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.30 % Allowed : 14.35 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.26), residues: 1025 helix: 2.67 (0.20), residues: 673 sheet: 0.86 (0.80), residues: 49 loop : 0.16 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 498 HIS 0.004 0.001 HIS L 7 PHE 0.015 0.001 PHE L 59 TYR 0.013 0.002 TYR B 51 ARG 0.006 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 1002) hydrogen bonds : angle 3.21899 ( 2493) covalent geometry : bond 0.00411 (16874) covalent geometry : angle 0.57287 (24363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8527 (tp30) cc_final: 0.8310 (tp30) REVERT: E 97 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7133 (mt-10) REVERT: H 42 TYR cc_start: 0.7896 (t80) cc_final: 0.7654 (t80) REVERT: K 10 PHE cc_start: 0.6925 (t80) cc_final: 0.6511 (t80) REVERT: K 50 LEU cc_start: 0.8085 (mt) cc_final: 0.7710 (mt) REVERT: L 6 LYS cc_start: 0.8862 (tttm) cc_final: 0.8264 (ptpp) REVERT: M 447 GLU cc_start: 0.8352 (mp0) cc_final: 0.7720 (mt-10) outliers start: 20 outliers final: 17 residues processed: 105 average time/residue: 0.2855 time to fit residues: 44.5433 Evaluate side-chains 104 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 518 ASN Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 109 HIS E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.054266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.037581 restraints weight = 125850.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.038425 restraints weight = 60011.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.038945 restraints weight = 39015.571| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16874 Z= 0.138 Angle : 0.544 10.354 24363 Z= 0.319 Chirality : 0.032 0.223 2742 Planarity : 0.003 0.039 1819 Dihedral : 29.809 178.211 5167 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.49 % Allowed : 15.04 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.27), residues: 1025 helix: 2.89 (0.20), residues: 672 sheet: 1.02 (0.84), residues: 48 loop : 0.28 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 498 HIS 0.004 0.001 HIS A 113 PHE 0.021 0.001 PHE L 49 TYR 0.011 0.001 TYR L 43 ARG 0.005 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1002) hydrogen bonds : angle 2.96144 ( 2493) covalent geometry : bond 0.00289 (16874) covalent geometry : angle 0.54411 (24363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7144 (mt-10) REVERT: F 88 TYR cc_start: 0.8946 (m-10) cc_final: 0.8728 (m-10) REVERT: H 42 TYR cc_start: 0.7681 (t80) cc_final: 0.7382 (t80) REVERT: K 10 PHE cc_start: 0.6817 (t80) cc_final: 0.6420 (t80) REVERT: L 6 LYS cc_start: 0.8856 (tttm) cc_final: 0.8330 (ptpp) REVERT: M 447 GLU cc_start: 0.8348 (mp0) cc_final: 0.7785 (mt-10) REVERT: M 453 ARG cc_start: 0.9194 (ttm170) cc_final: 0.8911 (ttm110) REVERT: M 482 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8293 (tpp80) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.3024 time to fit residues: 48.8422 Evaluate side-chains 105 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.054344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.037654 restraints weight = 126135.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.038500 restraints weight = 60293.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.039016 restraints weight = 39233.021| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16874 Z= 0.139 Angle : 0.547 9.079 24363 Z= 0.319 Chirality : 0.032 0.222 2742 Planarity : 0.003 0.040 1819 Dihedral : 29.757 178.028 5165 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.38 % Allowed : 15.73 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.27), residues: 1025 helix: 2.96 (0.20), residues: 673 sheet: 1.23 (0.85), residues: 48 loop : 0.33 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 498 HIS 0.004 0.001 HIS A 113 PHE 0.019 0.001 PHE K 59 TYR 0.012 0.001 TYR L 43 ARG 0.006 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1002) hydrogen bonds : angle 2.93749 ( 2493) covalent geometry : bond 0.00294 (16874) covalent geometry : angle 0.54683 (24363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8833 (mmm) cc_final: 0.8425 (mmm) REVERT: E 97 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7167 (mt-10) REVERT: F 88 TYR cc_start: 0.8942 (m-10) cc_final: 0.8700 (m-10) REVERT: H 42 TYR cc_start: 0.7673 (t80) cc_final: 0.7367 (t80) REVERT: K 10 PHE cc_start: 0.6884 (t80) cc_final: 0.6445 (t80) REVERT: L 6 LYS cc_start: 0.8808 (tttm) cc_final: 0.8329 (ptpp) REVERT: M 447 GLU cc_start: 0.8353 (mp0) cc_final: 0.7728 (mt-10) REVERT: M 482 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8223 (tpp80) REVERT: M 536 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8025 (mp0) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.3048 time to fit residues: 48.3787 Evaluate side-chains 103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.053515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.036675 restraints weight = 126789.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.037464 restraints weight = 61908.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.037970 restraints weight = 40715.330| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16874 Z= 0.188 Angle : 0.573 8.423 24363 Z= 0.333 Chirality : 0.033 0.219 2742 Planarity : 0.004 0.043 1819 Dihedral : 29.927 178.299 5165 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.84 % Allowed : 15.38 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.27), residues: 1025 helix: 2.91 (0.20), residues: 673 sheet: 1.10 (0.83), residues: 49 loop : 0.25 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 498 HIS 0.004 0.001 HIS L 7 PHE 0.018 0.001 PHE L 49 TYR 0.014 0.001 TYR B 51 ARG 0.005 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1002) hydrogen bonds : angle 3.11612 ( 2493) covalent geometry : bond 0.00413 (16874) covalent geometry : angle 0.57345 (24363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 97 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7153 (mt-10) REVERT: H 42 TYR cc_start: 0.7865 (t80) cc_final: 0.7574 (t80) REVERT: H 93 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8544 (mm-30) REVERT: K 10 PHE cc_start: 0.6860 (t80) cc_final: 0.6497 (t80) REVERT: L 6 LYS cc_start: 0.8790 (tttm) cc_final: 0.8333 (ptpp) REVERT: L 56 GLU cc_start: 0.8227 (tt0) cc_final: 0.7695 (pm20) REVERT: M 447 GLU cc_start: 0.8394 (mp0) cc_final: 0.7795 (mt-10) REVERT: M 482 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8128 (tpp80) REVERT: M 536 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8044 (mp0) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.2841 time to fit residues: 42.2097 Evaluate side-chains 99 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.053145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036708 restraints weight = 127056.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037516 restraints weight = 61827.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.037997 restraints weight = 40691.555| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16874 Z= 0.184 Angle : 0.592 15.216 24363 Z= 0.339 Chirality : 0.034 0.225 2742 Planarity : 0.004 0.044 1819 Dihedral : 29.969 178.025 5165 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.07 % Allowed : 15.96 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.26), residues: 1025 helix: 2.85 (0.19), residues: 671 sheet: 1.07 (0.83), residues: 49 loop : 0.11 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 498 HIS 0.004 0.001 HIS L 7 PHE 0.014 0.001 PHE L 49 TYR 0.013 0.001 TYR L 43 ARG 0.005 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 1002) hydrogen bonds : angle 3.15859 ( 2493) covalent geometry : bond 0.00405 (16874) covalent geometry : angle 0.59190 (24363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7810 (mtp) cc_final: 0.7553 (mtt) REVERT: E 97 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7101 (mt-10) REVERT: H 42 TYR cc_start: 0.7864 (t80) cc_final: 0.7577 (t80) REVERT: H 93 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8445 (mm-30) REVERT: K 10 PHE cc_start: 0.6821 (t80) cc_final: 0.6493 (t80) REVERT: L 6 LYS cc_start: 0.8796 (tttm) cc_final: 0.8309 (ptpp) REVERT: L 56 GLU cc_start: 0.8213 (tt0) cc_final: 0.7657 (pm20) REVERT: M 447 GLU cc_start: 0.8366 (mp0) cc_final: 0.7753 (mt-10) REVERT: M 482 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8150 (tpp80) REVERT: M 536 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7979 (mp0) outliers start: 18 outliers final: 15 residues processed: 100 average time/residue: 0.2775 time to fit residues: 41.4519 Evaluate side-chains 103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 106 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 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 = 0.3575 r_free = 0.3575 target = 0.053596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037065 restraints weight = 127581.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.037879 restraints weight = 61471.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.038397 restraints weight = 40317.370| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16874 Z= 0.156 Angle : 0.576 14.739 24363 Z= 0.332 Chirality : 0.033 0.222 2742 Planarity : 0.004 0.043 1819 Dihedral : 29.897 177.354 5165 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.49 % Allowed : 16.65 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.26), residues: 1025 helix: 2.85 (0.19), residues: 671 sheet: 1.03 (0.83), residues: 50 loop : 0.13 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 498 HIS 0.006 0.001 HIS K 7 PHE 0.016 0.001 PHE L 49 TYR 0.012 0.001 TYR L 43 ARG 0.006 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 1002) hydrogen bonds : angle 3.07466 ( 2493) covalent geometry : bond 0.00339 (16874) covalent geometry : angle 0.57567 (24363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7676 (mtp) cc_final: 0.7465 (mtt) REVERT: B 84 MET cc_start: 0.8593 (mmm) cc_final: 0.8271 (mmm) REVERT: H 42 TYR cc_start: 0.7793 (t80) cc_final: 0.7497 (t80) REVERT: H 93 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8472 (mm-30) REVERT: K 10 PHE cc_start: 0.6893 (t80) cc_final: 0.6551 (t80) REVERT: L 6 LYS cc_start: 0.8744 (tttm) cc_final: 0.8282 (ptpp) REVERT: M 447 GLU cc_start: 0.8367 (mp0) cc_final: 0.7745 (mt-10) REVERT: M 482 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8176 (tpp80) REVERT: M 536 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7969 (mp0) outliers start: 13 outliers final: 12 residues processed: 95 average time/residue: 0.2940 time to fit residues: 41.2675 Evaluate side-chains 99 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 75 ARG Chi-restraints excluded: chain K residue 78 PHE Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 445 VAL Chi-restraints excluded: chain M residue 497 ILE Chi-restraints excluded: chain M residue 536 GLU Chi-restraints excluded: chain M residue 538 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 HIS ** 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 = 0.3547 r_free = 0.3547 target = 0.052666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.036024 restraints weight = 127327.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.036807 restraints weight = 62407.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037280 restraints weight = 41334.744| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16874 Z= 0.228 Angle : 0.622 15.294 24363 Z= 0.355 Chirality : 0.035 0.223 2742 Planarity : 0.004 0.045 1819 Dihedral : 30.125 177.245 5165 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 16.88 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.26), residues: 1025 helix: 2.66 (0.19), residues: 670 sheet: 1.05 (0.82), residues: 49 loop : 0.01 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 498 HIS 0.005 0.001 HIS L 7 PHE 0.014 0.001 PHE L 49 TYR 0.016 0.002 TYR B 51 ARG 0.004 0.000 ARG K 60 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 1002) hydrogen bonds : angle 3.30054 ( 2493) covalent geometry : bond 0.00506 (16874) covalent geometry : angle 0.62170 (24363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5464.75 seconds wall clock time: 97 minutes 9.19 seconds (5829.19 seconds total)