Starting phenix.real_space_refine on Tue Nov 19 16:43:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gd0_51238/11_2024/9gd0_51238.cif" } resolution = 2.8 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= -0.005 sd= 1.153 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 500 5.49 5 S 22 5.16 5 C 11144 2.51 5 N 3776 2.21 5 O 4765 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-5513/modules/chem_data/mon_lib" Total number of atoms: 20207 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5090 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "J" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5160 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "K" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 592 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "N" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "O" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 12.05, per 1000 atoms: 0.60 Number of scatterers: 20207 At special positions: 0 Unit cell: (110.7, 124.23, 188.19, 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 22 16.00 P 500 15.00 O 4765 8.00 N 3776 7.00 C 11144 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: 4.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 17 sheets defined 75.3% alpha, 3.2% beta 247 base pairs and 498 stacking pairs defined. Time for finding SS restraints: 10.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.901A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.529A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.530A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.479A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.591A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.621A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.556A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.346A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.665A pdb=" N MET K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.199A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 97 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 removed outlier: 3.827A pdb=" N GLN N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.646A pdb=" N ILE N 58 " --> pdb=" O LYS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.659A pdb=" N THR N 93 " --> pdb=" O ARG N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 121 removed outlier: 3.527A pdb=" N SER N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.686A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.639A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.523A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL P 65 " --> pdb=" O PHE P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A 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: 6.303A 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: 6.941A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.762A 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: 6.976A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'K' and resid 83 through 84 removed outlier: 6.773A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.010A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.852A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'O' and resid 118 through 119 701 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 631 hydrogen bonds 1262 hydrogen bond angles 0 basepair planarities 247 basepair parallelities 498 stacking parallelities Total time for adding SS restraints: 10.86 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4650 1.34 - 1.45: 6452 1.45 - 1.57: 9444 1.57 - 1.69: 998 1.69 - 1.80: 40 Bond restraints: 21584 Sorted by residual: bond pdb=" N ARG F 92 " pdb=" CA ARG F 92 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.15e+00 bond pdb=" N ARG N 83 " pdb=" CA ARG N 83 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 5.98e+00 bond pdb=" N GLU N 32 " pdb=" CA GLU N 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 21579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 30386 2.19 - 4.37: 901 4.37 - 6.56: 16 6.56 - 8.74: 2 8.74 - 10.93: 4 Bond angle restraints: 31309 Sorted by residual: angle pdb=" O3' DA J 90 " pdb=" C3' DA J 90 " pdb=" C2' DA J 90 " ideal model delta sigma weight residual 111.50 100.57 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" O3' DC J 76 " pdb=" C3' DC J 76 " pdb=" C2' DC J 76 " ideal model delta sigma weight residual 111.50 102.60 8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" O3' DA I -57 " pdb=" C3' DA I -57 " pdb=" C2' DA I -57 " ideal model delta sigma weight residual 111.50 102.66 8.84 1.50e+00 4.44e-01 3.47e+01 angle pdb=" O3' DG I -56 " pdb=" C3' DG I -56 " pdb=" C2' DG I -56 " ideal model delta sigma weight residual 111.50 102.69 8.81 1.50e+00 4.44e-01 3.45e+01 angle pdb=" O3' DC J 75 " pdb=" C3' DC J 75 " pdb=" C2' DC J 75 " ideal model delta sigma weight residual 111.50 102.81 8.69 1.50e+00 4.44e-01 3.36e+01 ... (remaining 31304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7573 17.97 - 35.94: 1669 35.94 - 53.91: 2206 53.91 - 71.88: 229 71.88 - 89.85: 10 Dihedral angle restraints: 11687 sinusoidal: 8043 harmonic: 3644 Sorted by residual: dihedral pdb=" CA PRO N 100 " pdb=" C PRO N 100 " pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta harmonic sigma weight residual -180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE O 84 " pdb=" C PHE O 84 " pdb=" N GLN O 85 " pdb=" CA GLN O 85 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N THR L 30 " pdb=" CA THR L 30 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2426 0.052 - 0.104: 949 0.104 - 0.156: 188 0.156 - 0.208: 12 0.208 - 0.259: 3 Chirality restraints: 3578 Sorted by residual: chirality pdb=" C3' DA J 90 " pdb=" C4' DA J 90 " pdb=" O3' DA J 90 " pdb=" C2' DA J 90 " both_signs ideal model delta sigma weight residual False -2.66 -2.92 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' DC J 76 " pdb=" C4' DC J 76 " pdb=" O3' DC J 76 " pdb=" C2' DC J 76 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' DC J 75 " pdb=" C4' DC J 75 " pdb=" O3' DC J 75 " pdb=" C2' DC J 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3575 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C VAL B 70 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 71 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 67 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG L 67 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG L 67 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP L 68 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 51 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C TYR L 51 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR L 51 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU L 52 " 0.021 2.00e-02 2.50e+03 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2872 2.76 - 3.30: 16508 3.30 - 3.83: 38423 3.83 - 4.37: 49836 4.37 - 4.90: 69965 Nonbonded interactions: 177604 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 50 " pdb=" NH1 ARG B 39 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.346 3.040 nonbonded pdb=" NH1 ARG K 116 " pdb=" O THR K 118 " model vdw 2.358 3.120 nonbonded pdb=" NH1 ARG O 128 " pdb=" OE2 GLU O 133 " model vdw 2.389 3.120 ... (remaining 177599 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' selection = (chain 'O' and resid 39 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 97) selection = (chain 'F' and resid 25 through 97) selection = (chain 'L' and resid 25 through 97) selection = (chain 'P' and resid 25 through 97) } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 120) selection = (chain 'N' and resid 32 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 53.810 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.006 0.033 21584 Z= 0.305 Angle : 0.842 10.928 31309 Z= 0.545 Chirality : 0.054 0.259 3578 Planarity : 0.012 0.096 2225 Dihedral : 27.261 89.849 9331 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.21), residues: 1225 helix: -0.35 (0.15), residues: 928 sheet: None (None), residues: 0 loop : -0.03 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS F 75 PHE 0.016 0.003 PHE D 67 TYR 0.027 0.005 TYR M 57 ARG 0.017 0.003 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7508 (tt0) cc_final: 0.7251 (tt0) REVERT: C 57 TYR cc_start: 0.8459 (t80) cc_final: 0.7486 (t80) REVERT: M 114 VAL cc_start: 0.8668 (t) cc_final: 0.8429 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 2.0326 time to fit residues: 662.9445 Evaluate side-chains 217 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.0470 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 106 HIS E 93 GLN M 24 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21584 Z= 0.228 Angle : 0.620 7.802 31309 Z= 0.380 Chirality : 0.034 0.146 3578 Planarity : 0.004 0.039 2225 Dihedral : 30.504 72.916 6859 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.15 % Allowed : 12.77 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.77 (0.23), residues: 1225 helix: 1.58 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.010 0.001 PHE K 67 TYR 0.012 0.002 TYR B 51 ARG 0.009 0.001 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 41 GLU cc_start: 0.7610 (pm20) cc_final: 0.7018 (pm20) REVERT: H 43 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7944 (mmpt) REVERT: K 79 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (tmtt) REVERT: M 61 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6928 (tp30) outliers start: 33 outliers final: 7 residues processed: 254 average time/residue: 1.9610 time to fit residues: 541.0859 Evaluate side-chains 226 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain P residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 0.0270 chunk 152 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN B 93 GLN D 106 HIS ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21584 Z= 0.282 Angle : 0.602 9.621 31309 Z= 0.364 Chirality : 0.035 0.137 3578 Planarity : 0.005 0.039 2225 Dihedral : 30.405 71.265 6859 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.43 % Allowed : 14.30 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.17 (0.23), residues: 1225 helix: 1.93 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.14 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS M 31 PHE 0.012 0.002 PHE K 67 TYR 0.017 0.002 TYR B 88 ARG 0.014 0.001 ARG P 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8768 (mp) REVERT: F 92 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7797 (ttm-80) REVERT: K 79 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7448 (tmtt) REVERT: K 99 TYR cc_start: 0.8298 (t80) cc_final: 0.7817 (t80) REVERT: O 41 TYR cc_start: 0.8586 (m-80) cc_final: 0.8326 (m-80) REVERT: O 90 MET cc_start: 0.6701 (mtp) cc_final: 0.6349 (mtp) outliers start: 36 outliers final: 16 residues processed: 243 average time/residue: 2.0371 time to fit residues: 537.6339 Evaluate side-chains 234 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21584 Z= 0.206 Angle : 0.569 9.845 31309 Z= 0.346 Chirality : 0.033 0.150 3578 Planarity : 0.004 0.038 2225 Dihedral : 30.059 71.761 6859 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.67 % Allowed : 16.21 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.51 (0.23), residues: 1225 helix: 2.21 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.16 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.001 PHE O 78 TYR 0.017 0.002 TYR B 88 ARG 0.008 0.001 ARG P 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8891 (mp) REVERT: F 92 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7750 (ttm-80) REVERT: F 93 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: H 43 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: K 79 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7372 (tmtt) REVERT: O 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8288 (m-80) outliers start: 28 outliers final: 11 residues processed: 244 average time/residue: 1.9376 time to fit residues: 514.2641 Evaluate side-chains 232 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN N 81 ASN O 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21584 Z= 0.195 Angle : 0.560 10.243 31309 Z= 0.341 Chirality : 0.033 0.152 3578 Planarity : 0.004 0.040 2225 Dihedral : 29.794 70.677 6859 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.05 % Allowed : 16.30 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.75 (0.23), residues: 1225 helix: 2.38 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.09 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE O 78 TYR 0.017 0.001 TYR B 88 ARG 0.009 0.001 ARG P 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 96 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7733 (mtt-85) REVERT: F 92 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7739 (ttm-80) REVERT: H 43 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8108 (ttmm) REVERT: H 60 ASN cc_start: 0.8415 (t0) cc_final: 0.8190 (t0) REVERT: H 73 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: K 133 GLU cc_start: 0.5937 (mt-10) cc_final: 0.5720 (mt-10) REVERT: O 41 TYR cc_start: 0.8547 (m-80) cc_final: 0.8268 (m-80) outliers start: 32 outliers final: 11 residues processed: 243 average time/residue: 1.9471 time to fit residues: 515.8120 Evaluate side-chains 228 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 135 optimal weight: 0.0060 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21584 Z= 0.187 Angle : 0.562 9.364 31309 Z= 0.341 Chirality : 0.032 0.151 3578 Planarity : 0.004 0.038 2225 Dihedral : 29.750 70.717 6859 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.10 % Allowed : 17.54 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.89 (0.23), residues: 1225 helix: 2.49 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.03 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 106 PHE 0.009 0.001 PHE K 67 TYR 0.016 0.001 TYR B 88 ARG 0.009 0.001 ARG P 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8822 (mt) REVERT: F 92 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7714 (ttm-80) REVERT: F 93 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: H 60 ASN cc_start: 0.8395 (t0) cc_final: 0.8176 (t0) REVERT: H 65 ASP cc_start: 0.8492 (t0) cc_final: 0.8183 (t0) REVERT: H 73 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: O 41 TYR cc_start: 0.8547 (m-80) cc_final: 0.8260 (m-80) outliers start: 22 outliers final: 9 residues processed: 238 average time/residue: 1.8459 time to fit residues: 480.5447 Evaluate side-chains 230 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain P residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.0570 chunk 93 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 137 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21584 Z= 0.235 Angle : 0.577 9.998 31309 Z= 0.348 Chirality : 0.034 0.151 3578 Planarity : 0.004 0.045 2225 Dihedral : 29.921 70.815 6859 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.10 % Allowed : 18.88 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.76 (0.23), residues: 1225 helix: 2.39 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.08 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE K 67 TYR 0.028 0.002 TYR B 88 ARG 0.009 0.000 ARG P 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8344 (tp40) cc_final: 0.8096 (tp-100) REVERT: C 102 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8689 (mt) REVERT: D 54 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7719 (mptt) REVERT: F 92 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7765 (ttm-80) REVERT: H 43 LYS cc_start: 0.8353 (tppt) cc_final: 0.8023 (mmpt) REVERT: H 73 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: K 79 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7404 (tmtt) REVERT: O 41 TYR cc_start: 0.8563 (m-80) cc_final: 0.8274 (m-80) REVERT: O 90 MET cc_start: 0.6728 (mtt) cc_final: 0.6463 (mtp) REVERT: O 94 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6427 (mp0) outliers start: 22 outliers final: 10 residues processed: 232 average time/residue: 1.9417 time to fit residues: 490.8355 Evaluate side-chains 232 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21584 Z= 0.289 Angle : 0.607 10.408 31309 Z= 0.363 Chirality : 0.036 0.154 3578 Planarity : 0.004 0.036 2225 Dihedral : 30.173 71.881 6859 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.29 % Allowed : 19.07 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.57 (0.23), residues: 1225 helix: 2.26 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 31 PHE 0.015 0.001 PHE K 67 TYR 0.033 0.002 TYR B 88 ARG 0.009 0.001 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8428 (m-40) cc_final: 0.8169 (m110) REVERT: C 75 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8552 (mmmm) REVERT: C 102 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8703 (mt) REVERT: D 54 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7740 (mptt) REVERT: F 92 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7774 (ttm-80) REVERT: H 73 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: O 41 TYR cc_start: 0.8578 (m-80) cc_final: 0.8290 (m-80) REVERT: O 94 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6617 (mp0) outliers start: 24 outliers final: 12 residues processed: 235 average time/residue: 1.9562 time to fit residues: 500.2889 Evaluate side-chains 234 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21584 Z= 0.247 Angle : 0.605 11.798 31309 Z= 0.361 Chirality : 0.035 0.154 3578 Planarity : 0.005 0.091 2225 Dihedral : 30.165 72.575 6859 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 19.54 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.60 (0.23), residues: 1225 helix: 2.28 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 106 PHE 0.011 0.001 PHE K 67 TYR 0.038 0.002 TYR B 88 ARG 0.011 0.001 ARG N 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8421 (m-40) cc_final: 0.8157 (m110) REVERT: C 102 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8702 (mt) REVERT: D 54 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7724 (mptt) REVERT: F 92 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7783 (ttm-80) REVERT: F 93 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: H 43 LYS cc_start: 0.8367 (tppt) cc_final: 0.8132 (mmtm) REVERT: H 65 ASP cc_start: 0.8552 (t0) cc_final: 0.8241 (t0) REVERT: H 73 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: O 41 TYR cc_start: 0.8571 (m-80) cc_final: 0.8282 (m-80) REVERT: O 94 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6639 (mp0) outliers start: 21 outliers final: 11 residues processed: 230 average time/residue: 1.9257 time to fit residues: 483.0258 Evaluate side-chains 236 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN L 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21584 Z= 0.319 Angle : 0.633 11.724 31309 Z= 0.375 Chirality : 0.037 0.154 3578 Planarity : 0.005 0.050 2225 Dihedral : 30.355 78.473 6859 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.91 % Allowed : 20.31 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.34 (0.23), residues: 1225 helix: 2.10 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -0.31 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 31 PHE 0.012 0.002 PHE K 67 TYR 0.034 0.002 TYR B 88 ARG 0.014 0.001 ARG P 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m-40) cc_final: 0.8218 (m110) REVERT: C 75 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8564 (mmmm) REVERT: C 102 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8669 (mt) REVERT: D 54 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7753 (mptt) REVERT: F 92 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7873 (ttm-80) REVERT: F 93 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7029 (mp10) REVERT: H 43 LYS cc_start: 0.8428 (tppt) cc_final: 0.8100 (mmpt) REVERT: H 65 ASP cc_start: 0.8507 (t0) cc_final: 0.8224 (t0) REVERT: H 73 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: O 41 TYR cc_start: 0.8565 (m-80) cc_final: 0.8267 (m-80) REVERT: O 90 MET cc_start: 0.6660 (mtp) cc_final: 0.5939 (mtp) REVERT: O 94 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6547 (mp0) outliers start: 20 outliers final: 13 residues processed: 233 average time/residue: 1.9679 time to fit residues: 500.6699 Evaluate side-chains 236 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 106 HIS G 104 GLN L 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.112181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.082551 restraints weight = 45377.903| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.53 r_work: 0.3193 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21584 Z= 0.223 Angle : 0.628 11.247 31309 Z= 0.372 Chirality : 0.035 0.149 3578 Planarity : 0.005 0.055 2225 Dihedral : 30.353 78.986 6859 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.10 % Allowed : 20.02 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.43 (0.23), residues: 1225 helix: 2.17 (0.17), residues: 941 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 106 PHE 0.011 0.001 PHE K 67 TYR 0.051 0.002 TYR B 88 ARG 0.014 0.001 ARG B 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8037.32 seconds wall clock time: 211 minutes 45.43 seconds (12705.43 seconds total)