Starting phenix.real_space_refine on Wed Sep 17 21:48:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qaj_52975/09_2025/9qaj_52975.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 288 5.49 5 S 12 5.16 5 C 6714 2.51 5 N 2285 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12144 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" 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: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 3.04, per 1000 atoms: 0.25 Number of scatterers: 12144 At special positions: 0 Unit cell: (123.201, 98.415, 114.453, 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 12 16.00 P 288 15.00 O 2845 8.00 N 2285 7.00 C 6714 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: 1.02 Conformation dependent library (CDL) restraints added in 377.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 75.5% alpha, 3.0% beta 141 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A 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 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.435A 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 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 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 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 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.755A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.509A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.461A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (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 3 through 10 removed outlier: 3.531A pdb=" N THR K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 26 removed outlier: 3.793A pdb=" N GLU L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.532A pdb=" N THR M 10 " --> pdb=" O VAL M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.824A pdb=" N VAL N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.708A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A 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 removed outlier: 6.949A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A 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: 7.477A 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 78 436 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2690 1.33 - 1.45: 3999 1.45 - 1.57: 5655 1.57 - 1.69: 576 1.69 - 1.81: 22 Bond restraints: 12942 Sorted by residual: bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.31e+00 bond pdb=" C4' DG J 2 " pdb=" C3' DG J 2 " ideal model delta sigma weight residual 1.523 1.503 0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 9.22e-01 bond pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.87e-01 bond pdb=" CA ARG B 95 " pdb=" C ARG B 95 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.08e-02 8.57e+03 8.82e-01 ... (remaining 12937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 18051 1.42 - 2.83: 619 2.83 - 4.25: 44 4.25 - 5.66: 11 5.66 - 7.08: 3 Bond angle restraints: 18728 Sorted by residual: angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.32e+00 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 119.78 -7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" CB GLU D 76 " pdb=" CG GLU D 76 " pdb=" CD GLU D 76 " ideal model delta sigma weight residual 112.60 116.44 -3.84 1.70e+00 3.46e-01 5.11e+00 angle pdb=" C GLY C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.10e+00 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 5014 25.88 - 51.77: 1577 51.77 - 77.65: 440 77.65 - 103.54: 6 103.54 - 129.42: 1 Dihedral angle restraints: 7038 sinusoidal: 4732 harmonic: 2306 Sorted by residual: dihedral pdb=" C4' DC J -38 " pdb=" C3' DC J -38 " pdb=" O3' DC J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 90.58 129.42 1 3.50e+01 8.16e-04 1.28e+01 dihedral pdb=" CA ARG M 7 " pdb=" CB ARG M 7 " pdb=" CG ARG M 7 " pdb=" CD ARG M 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.40 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG K 7 " pdb=" CB ARG K 7 " pdb=" CG ARG K 7 " pdb=" CD ARG K 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.38 59.38 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1463 0.030 - 0.060: 515 0.060 - 0.089: 115 0.089 - 0.119: 37 0.119 - 0.149: 11 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2138 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.023 2.00e-02 2.50e+03 9.23e-03 2.56e+00 pdb=" N9 DG I -35 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 17 " 0.020 2.00e-02 2.50e+03 9.30e-03 2.38e+00 pdb=" N9 DA J 17 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 17 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 17 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA J 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA J 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 17 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA J 17 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -49 " -0.018 2.00e-02 2.50e+03 8.66e-03 2.25e+00 pdb=" N9 DG J -49 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J -49 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -49 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J -49 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG J -49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG J -49 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG J -49 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG J -49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 590 2.70 - 3.25: 11214 3.25 - 3.80: 23934 3.80 - 4.35: 28428 4.35 - 4.90: 41259 Nonbonded interactions: 105425 Sorted by model distance: nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.164 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.165 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU G 64 " pdb=" NH1 ARG M 7 " model vdw 2.196 3.120 ... (remaining 105420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 36 through 124) selection = (chain 'H' and resid 36 through 124) } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 1.160 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 : 0.005 0.051 12942 Z= 0.221 Angle : 0.580 7.078 18728 Z= 0.349 Chirality : 0.034 0.149 2141 Planarity : 0.003 0.030 1371 Dihedral : 28.272 129.423 5546 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.32 % Allowed : 19.24 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.31), residues: 772 helix: 2.75 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.018 0.001 TYR G 50 PHE 0.016 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00491 (12942) covalent geometry : angle 0.57990 (18728) hydrogen bonds : bond 0.10853 ( 796) hydrogen bonds : angle 3.81554 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.325 Fit side-chains REVERT: B 59 LYS cc_start: 0.9159 (tttm) cc_final: 0.8804 (tppp) REVERT: B 63 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 92 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 46 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8668 (mmmt) REVERT: H 71 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7976 (mm-30) outliers start: 2 outliers final: 5 residues processed: 224 average time/residue: 0.7208 time to fit residues: 172.1974 Evaluate side-chains 212 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 74 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 104 GLN C 112 GLN F 93 GLN G 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.036452 restraints weight = 44230.549| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.84 r_work: 0.2405 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12942 Z= 0.211 Angle : 0.561 5.484 18728 Z= 0.337 Chirality : 0.033 0.150 2141 Planarity : 0.004 0.038 1371 Dihedral : 30.868 129.705 4061 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.74 % Allowed : 24.76 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.31), residues: 772 helix: 2.80 (0.22), residues: 585 sheet: None (None), residues: 0 loop : -1.53 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.015 0.001 TYR G 57 PHE 0.016 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (12942) covalent geometry : angle 0.56104 (18728) hydrogen bonds : bond 0.03901 ( 796) hydrogen bonds : angle 3.10319 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 0.357 Fit side-chains REVERT: B 59 LYS cc_start: 0.9292 (tttm) cc_final: 0.8956 (tppp) REVERT: B 63 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8909 (mt-10) REVERT: C 56 GLU cc_start: 0.9278 (tt0) cc_final: 0.9000 (tt0) REVERT: C 90 ASP cc_start: 0.8538 (t70) cc_final: 0.8046 (t0) REVERT: C 92 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8707 (mt-10) REVERT: D 68 ASP cc_start: 0.9450 (t0) cc_final: 0.9246 (t0) REVERT: E 59 GLU cc_start: 0.8970 (pm20) cc_final: 0.8762 (pm20) REVERT: G 39 TYR cc_start: 0.9364 (m-80) cc_final: 0.9070 (m-80) REVERT: G 41 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8273 (tm-30) REVERT: G 64 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9043 (tm-30) REVERT: H 33 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7952 (mmm160) REVERT: H 34 LYS cc_start: 0.9062 (mppt) cc_final: 0.8799 (mppt) REVERT: H 46 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8944 (mmmt) REVERT: H 68 ASP cc_start: 0.9540 (t0) cc_final: 0.9299 (t0) REVERT: H 71 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9075 (mm-30) REVERT: H 105 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8374 (tm-30) outliers start: 11 outliers final: 7 residues processed: 232 average time/residue: 0.6991 time to fit residues: 173.4217 Evaluate side-chains 211 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN E 113 HIS G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.037870 restraints weight = 43510.258| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.88 r_work: 0.2446 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12942 Z= 0.152 Angle : 0.539 5.950 18728 Z= 0.325 Chirality : 0.032 0.145 2141 Planarity : 0.004 0.039 1371 Dihedral : 30.703 130.112 4055 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.15 % Allowed : 25.39 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.30), residues: 772 helix: 2.87 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.015 0.001 TYR G 57 PHE 0.011 0.001 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (12942) covalent geometry : angle 0.53943 (18728) hydrogen bonds : bond 0.03350 ( 796) hydrogen bonds : angle 2.85821 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.326 Fit side-chains REVERT: B 59 LYS cc_start: 0.9225 (tttm) cc_final: 0.8816 (tppp) REVERT: B 63 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8782 (mt-10) REVERT: B 88 TYR cc_start: 0.9394 (m-80) cc_final: 0.9145 (m-80) REVERT: C 56 GLU cc_start: 0.9258 (tt0) cc_final: 0.8937 (tt0) REVERT: C 64 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8805 (tm-30) REVERT: C 90 ASP cc_start: 0.8529 (t70) cc_final: 0.8162 (t0) REVERT: C 92 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8741 (mt-10) REVERT: D 68 ASP cc_start: 0.9414 (t0) cc_final: 0.9185 (t0) REVERT: D 86 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8435 (tpp80) REVERT: D 93 GLU cc_start: 0.9119 (mp0) cc_final: 0.8812 (mm-30) REVERT: E 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8572 (pm20) REVERT: G 41 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8049 (tm-30) REVERT: G 64 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9032 (tm-30) REVERT: G 90 ASP cc_start: 0.8960 (t0) cc_final: 0.8747 (t0) REVERT: H 34 LYS cc_start: 0.9049 (mppt) cc_final: 0.8626 (mmpt) REVERT: H 46 LYS cc_start: 0.9165 (mmmt) cc_final: 0.8924 (mmmt) REVERT: H 68 ASP cc_start: 0.9564 (t0) cc_final: 0.9277 (t0) REVERT: H 71 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9135 (mm-30) REVERT: H 105 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8184 (tm-30) outliers start: 20 outliers final: 7 residues processed: 240 average time/residue: 0.6344 time to fit residues: 163.7380 Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.035514 restraints weight = 44918.848| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 2.88 r_work: 0.2374 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12942 Z= 0.308 Angle : 0.602 6.412 18728 Z= 0.357 Chirality : 0.036 0.158 2141 Planarity : 0.004 0.037 1371 Dihedral : 30.956 130.315 4055 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.94 % Allowed : 27.60 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.31), residues: 772 helix: 2.92 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.40 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 92 TYR 0.019 0.002 TYR G 50 PHE 0.016 0.002 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00690 (12942) covalent geometry : angle 0.60227 (18728) hydrogen bonds : bond 0.04243 ( 796) hydrogen bonds : angle 3.13419 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.319 Fit side-chains REVERT: B 59 LYS cc_start: 0.9350 (tttm) cc_final: 0.9048 (tppp) REVERT: B 63 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8961 (mt-10) REVERT: C 56 GLU cc_start: 0.9295 (tt0) cc_final: 0.8904 (tt0) REVERT: C 64 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8934 (tm-30) REVERT: C 90 ASP cc_start: 0.8676 (t70) cc_final: 0.8192 (t0) REVERT: C 92 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8561 (mt-10) REVERT: D 68 ASP cc_start: 0.9459 (t0) cc_final: 0.9155 (t0) REVERT: D 86 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8445 (tpp80) REVERT: D 93 GLU cc_start: 0.9231 (mp0) cc_final: 0.8984 (mp0) REVERT: E 59 GLU cc_start: 0.8993 (pm20) cc_final: 0.8710 (pm20) REVERT: G 41 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 64 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.9074 (tm-30) REVERT: G 90 ASP cc_start: 0.9074 (t0) cc_final: 0.8857 (t0) REVERT: H 34 LYS cc_start: 0.9110 (mppt) cc_final: 0.8721 (mmpt) REVERT: H 46 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8990 (mmmt) REVERT: H 68 ASP cc_start: 0.9552 (t0) cc_final: 0.9260 (t0) REVERT: H 71 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9106 (mm-30) REVERT: H 105 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8383 (tm-30) outliers start: 25 outliers final: 15 residues processed: 218 average time/residue: 0.6786 time to fit residues: 157.9418 Evaluate side-chains 215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.037371 restraints weight = 43639.161| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.89 r_work: 0.2428 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12942 Z= 0.167 Angle : 0.558 6.449 18728 Z= 0.332 Chirality : 0.033 0.144 2141 Planarity : 0.004 0.038 1371 Dihedral : 30.759 129.825 4055 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.00 % Allowed : 28.39 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.31), residues: 772 helix: 2.95 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 92 TYR 0.018 0.001 TYR G 50 PHE 0.012 0.001 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (12942) covalent geometry : angle 0.55807 (18728) hydrogen bonds : bond 0.03405 ( 796) hydrogen bonds : angle 2.85449 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.371 Fit side-chains REVERT: A 105 GLU cc_start: 0.9172 (tt0) cc_final: 0.8955 (tp30) REVERT: B 59 LYS cc_start: 0.9255 (tttm) cc_final: 0.8886 (tppp) REVERT: B 63 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8818 (mt-10) REVERT: C 56 GLU cc_start: 0.9273 (tt0) cc_final: 0.8866 (tt0) REVERT: C 64 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8835 (tm-30) REVERT: C 90 ASP cc_start: 0.8561 (t70) cc_final: 0.8270 (t0) REVERT: C 92 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8796 (mt-10) REVERT: D 68 ASP cc_start: 0.9426 (t0) cc_final: 0.9141 (t0) REVERT: D 86 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8422 (tpp80) REVERT: D 93 GLU cc_start: 0.9203 (mp0) cc_final: 0.8915 (mp0) REVERT: E 59 GLU cc_start: 0.8919 (pm20) cc_final: 0.8608 (pm20) REVERT: G 41 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8090 (tm-30) REVERT: G 64 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.9037 (tm-30) REVERT: G 90 ASP cc_start: 0.9004 (t0) cc_final: 0.8753 (t0) REVERT: H 34 LYS cc_start: 0.9097 (mppt) cc_final: 0.8676 (mmpt) REVERT: H 46 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8927 (mmmt) REVERT: H 68 ASP cc_start: 0.9554 (t0) cc_final: 0.9260 (t0) REVERT: H 71 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9117 (mm-30) REVERT: H 105 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8218 (tm-30) outliers start: 19 outliers final: 7 residues processed: 226 average time/residue: 0.6462 time to fit residues: 156.6996 Evaluate side-chains 221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 212 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN D 95 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.036639 restraints weight = 44679.071| |-----------------------------------------------------------------------------| r_work (start): 0.2615 rms_B_bonded: 2.85 r_work: 0.2414 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12942 Z= 0.215 Angle : 0.575 7.927 18728 Z= 0.340 Chirality : 0.034 0.158 2141 Planarity : 0.004 0.038 1371 Dihedral : 30.832 130.038 4055 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.00 % Allowed : 28.55 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.31), residues: 772 helix: 2.99 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.021 0.002 TYR G 50 PHE 0.013 0.001 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00480 (12942) covalent geometry : angle 0.57522 (18728) hydrogen bonds : bond 0.03709 ( 796) hydrogen bonds : angle 2.92354 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8257 (tppp) REVERT: A 105 GLU cc_start: 0.9194 (tt0) cc_final: 0.8984 (tp30) REVERT: B 59 LYS cc_start: 0.9313 (tttm) cc_final: 0.9066 (tppp) REVERT: C 56 GLU cc_start: 0.9277 (tt0) cc_final: 0.8848 (tt0) REVERT: C 64 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8862 (tm-30) REVERT: C 90 ASP cc_start: 0.8685 (t70) cc_final: 0.8164 (t0) REVERT: C 92 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8490 (mt-10) REVERT: D 68 ASP cc_start: 0.9421 (t0) cc_final: 0.9110 (t0) REVERT: D 86 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8469 (tpp80) REVERT: D 93 GLU cc_start: 0.9206 (mp0) cc_final: 0.8886 (mp0) REVERT: E 59 GLU cc_start: 0.8960 (pm20) cc_final: 0.8636 (pm20) REVERT: G 41 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8102 (tm-30) REVERT: G 64 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9074 (tm-30) REVERT: G 90 ASP cc_start: 0.9040 (t0) cc_final: 0.8785 (t0) REVERT: H 34 LYS cc_start: 0.9152 (mppt) cc_final: 0.8705 (mmpt) REVERT: H 46 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8935 (mmmt) REVERT: H 68 ASP cc_start: 0.9537 (t0) cc_final: 0.9229 (t0) REVERT: H 71 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9103 (mm-30) REVERT: H 105 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8242 (tm-30) outliers start: 19 outliers final: 12 residues processed: 224 average time/residue: 0.6661 time to fit residues: 159.6992 Evaluate side-chains 223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.038285 restraints weight = 43284.560| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 2.88 r_work: 0.2458 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12942 Z= 0.157 Angle : 0.578 9.593 18728 Z= 0.339 Chirality : 0.032 0.157 2141 Planarity : 0.004 0.039 1371 Dihedral : 30.677 129.682 4055 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.05 % Allowed : 29.81 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.30), residues: 772 helix: 3.02 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 92 TYR 0.023 0.001 TYR G 50 PHE 0.010 0.001 PHE F 100 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (12942) covalent geometry : angle 0.57848 (18728) hydrogen bonds : bond 0.03304 ( 796) hydrogen bonds : angle 2.78346 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.325 Fit side-chains REVERT: A 105 GLU cc_start: 0.9149 (tt0) cc_final: 0.8941 (tp30) REVERT: B 59 LYS cc_start: 0.9224 (tttm) cc_final: 0.9024 (tppp) REVERT: C 56 GLU cc_start: 0.9270 (tt0) cc_final: 0.8835 (tt0) REVERT: C 64 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 90 ASP cc_start: 0.8599 (t70) cc_final: 0.7938 (t0) REVERT: C 92 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8723 (mp0) REVERT: D 68 ASP cc_start: 0.9420 (t0) cc_final: 0.9163 (t0) REVERT: D 86 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8452 (tpp80) REVERT: D 93 GLU cc_start: 0.9198 (mp0) cc_final: 0.8847 (mp0) REVERT: E 59 GLU cc_start: 0.8896 (pm20) cc_final: 0.8559 (pm20) REVERT: E 107 THR cc_start: 0.9771 (m) cc_final: 0.9535 (p) REVERT: G 64 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9033 (tm-30) REVERT: G 90 ASP cc_start: 0.9019 (t0) cc_final: 0.8742 (t0) REVERT: H 34 LYS cc_start: 0.9120 (mppt) cc_final: 0.8649 (mmpt) REVERT: H 46 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8916 (mmmt) REVERT: H 68 ASP cc_start: 0.9556 (t0) cc_final: 0.9261 (t0) REVERT: H 71 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9096 (mm-30) REVERT: H 93 GLU cc_start: 0.9076 (mp0) cc_final: 0.8808 (mp0) REVERT: H 105 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8110 (tm-30) outliers start: 13 outliers final: 8 residues processed: 229 average time/residue: 0.6568 time to fit residues: 161.1894 Evaluate side-chains 225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.035730 restraints weight = 45045.953| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 2.88 r_work: 0.2383 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12942 Z= 0.283 Angle : 0.618 10.200 18728 Z= 0.361 Chirality : 0.036 0.167 2141 Planarity : 0.004 0.044 1371 Dihedral : 30.946 129.823 4055 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.31 % Allowed : 29.18 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.31), residues: 772 helix: 3.01 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 79 TYR 0.025 0.002 TYR G 50 PHE 0.012 0.002 PHE F 100 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00636 (12942) covalent geometry : angle 0.61849 (18728) hydrogen bonds : bond 0.04127 ( 796) hydrogen bonds : angle 3.06088 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9192 (tt0) cc_final: 0.8982 (tp30) REVERT: C 56 GLU cc_start: 0.9295 (tt0) cc_final: 0.8964 (tt0) REVERT: C 64 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8944 (tm-30) REVERT: C 90 ASP cc_start: 0.8557 (t70) cc_final: 0.8292 (t0) REVERT: C 92 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8513 (mt-10) REVERT: D 68 ASP cc_start: 0.9440 (t0) cc_final: 0.9142 (t0) REVERT: D 86 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8456 (tpp80) REVERT: D 93 GLU cc_start: 0.9253 (mp0) cc_final: 0.9026 (mp0) REVERT: D 105 GLU cc_start: 0.8769 (tp30) cc_final: 0.8362 (tp30) REVERT: E 59 GLU cc_start: 0.8989 (pm20) cc_final: 0.8647 (pm20) REVERT: G 64 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9077 (tm-30) REVERT: G 90 ASP cc_start: 0.9057 (t0) cc_final: 0.8803 (t0) REVERT: H 34 LYS cc_start: 0.9132 (mppt) cc_final: 0.8653 (mmpt) REVERT: H 46 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8945 (mmmt) REVERT: H 68 ASP cc_start: 0.9541 (t0) cc_final: 0.9249 (t0) REVERT: H 71 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9085 (mm-30) REVERT: H 93 GLU cc_start: 0.9126 (mp0) cc_final: 0.8690 (mp0) REVERT: H 105 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8319 (tm-30) outliers start: 21 outliers final: 13 residues processed: 217 average time/residue: 0.7095 time to fit residues: 164.7642 Evaluate side-chains 221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 0.0370 chunk 73 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 3.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.036702 restraints weight = 44341.557| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.86 r_work: 0.2415 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12942 Z= 0.202 Angle : 0.608 9.977 18728 Z= 0.354 Chirality : 0.034 0.158 2141 Planarity : 0.004 0.046 1371 Dihedral : 30.838 129.447 4055 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.05 % Allowed : 31.07 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.31), residues: 772 helix: 2.98 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 92 TYR 0.026 0.002 TYR G 50 PHE 0.013 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00451 (12942) covalent geometry : angle 0.60824 (18728) hydrogen bonds : bond 0.03623 ( 796) hydrogen bonds : angle 2.93604 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8386 (tppp) cc_final: 0.8042 (ttpt) REVERT: A 105 GLU cc_start: 0.9162 (tt0) cc_final: 0.8958 (tp30) REVERT: C 56 GLU cc_start: 0.9283 (tt0) cc_final: 0.8957 (tt0) REVERT: C 64 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8870 (tm-30) REVERT: C 90 ASP cc_start: 0.8659 (t70) cc_final: 0.8019 (t0) REVERT: C 92 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8695 (mp0) REVERT: D 68 ASP cc_start: 0.9427 (t0) cc_final: 0.9152 (t0) REVERT: D 86 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8453 (tpp80) REVERT: D 93 GLU cc_start: 0.9210 (mp0) cc_final: 0.8977 (mp0) REVERT: E 59 GLU cc_start: 0.8955 (pm20) cc_final: 0.8613 (pm20) REVERT: G 64 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9055 (tm-30) REVERT: G 90 ASP cc_start: 0.9030 (t0) cc_final: 0.8769 (t0) REVERT: H 34 LYS cc_start: 0.9155 (mppt) cc_final: 0.8666 (mmpt) REVERT: H 46 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8962 (mmmt) REVERT: H 68 ASP cc_start: 0.9529 (t0) cc_final: 0.9228 (t0) REVERT: H 71 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9087 (mm-30) REVERT: H 93 GLU cc_start: 0.9092 (mp0) cc_final: 0.8667 (mp0) REVERT: H 105 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8364 (tm-30) outliers start: 13 outliers final: 11 residues processed: 220 average time/residue: 0.6834 time to fit residues: 160.8854 Evaluate side-chains 222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.0050 chunk 97 optimal weight: 10.0000 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.036896 restraints weight = 44729.233| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 2.86 r_work: 0.2423 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12942 Z= 0.192 Angle : 0.602 11.798 18728 Z= 0.351 Chirality : 0.033 0.153 2141 Planarity : 0.004 0.054 1371 Dihedral : 30.813 129.512 4055 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.21 % Allowed : 31.70 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.04 (0.31), residues: 772 helix: 2.97 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.026 0.002 TYR G 50 PHE 0.011 0.001 PHE F 100 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00428 (12942) covalent geometry : angle 0.60154 (18728) hydrogen bonds : bond 0.03602 ( 796) hydrogen bonds : angle 2.92077 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9280 (tt0) cc_final: 0.8957 (tt0) REVERT: C 64 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 90 ASP cc_start: 0.8467 (t70) cc_final: 0.8246 (t0) REVERT: C 92 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: D 68 ASP cc_start: 0.9419 (t0) cc_final: 0.9151 (t0) REVERT: D 86 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8461 (tpp80) REVERT: D 93 GLU cc_start: 0.9207 (mp0) cc_final: 0.8974 (mp0) REVERT: D 105 GLU cc_start: 0.8637 (tp30) cc_final: 0.7680 (tm-30) REVERT: E 59 GLU cc_start: 0.8950 (pm20) cc_final: 0.8607 (pm20) REVERT: G 64 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.9056 (tm-30) REVERT: G 90 ASP cc_start: 0.8998 (t0) cc_final: 0.8723 (t0) REVERT: H 34 LYS cc_start: 0.9148 (mppt) cc_final: 0.8650 (mmpt) REVERT: H 46 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8942 (mmmt) REVERT: H 68 ASP cc_start: 0.9531 (t0) cc_final: 0.9236 (t0) REVERT: H 71 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9075 (mm-30) REVERT: H 93 GLU cc_start: 0.9091 (mp0) cc_final: 0.8671 (mp0) REVERT: H 105 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8285 (tm-30) outliers start: 14 outliers final: 12 residues processed: 215 average time/residue: 0.6529 time to fit residues: 150.7742 Evaluate side-chains 222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 33 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.036277 restraints weight = 44822.357| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 2.90 r_work: 0.2401 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12942 Z= 0.246 Angle : 0.628 11.029 18728 Z= 0.365 Chirality : 0.035 0.169 2141 Planarity : 0.004 0.049 1371 Dihedral : 30.868 129.453 4055 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.05 % Allowed : 31.70 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.31), residues: 772 helix: 2.97 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.026 0.002 TYR G 50 PHE 0.013 0.002 PHE F 100 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00552 (12942) covalent geometry : angle 0.62816 (18728) hydrogen bonds : bond 0.03913 ( 796) hydrogen bonds : angle 3.01006 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4295.28 seconds wall clock time: 73 minutes 42.93 seconds (4422.93 seconds total)