Starting phenix.real_space_refine on Sun May 18 05:11:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.map" model { file = "/net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uw1_42636/05_2025/8uw1_42636.cif" } resolution = 2.88 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5964 atoms to isotropic. 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 292 5.49 5 S 13 5.16 5 C 6726 2.51 5 N 2282 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12164 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 745 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 29} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 7.18, per 1000 atoms: 0.59 Number of scatterers: 12164 At special positions: 0 Unit cell: (84.15, 120.7, 119.85, 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 13 16.00 P 292 15.00 O 2851 8.00 N 2282 7.00 C 6726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 913.5 milliseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 68.7% alpha, 3.1% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.594A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.592A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.588A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.667A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.592A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.517A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.790A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.690A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.517A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.770A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.625A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.722A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 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 removed outlier: 3.540A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.825A 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: 7.308A 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: 6.821A 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: 7.300A 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 78 394 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 3.33 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: 2103 1.33 - 1.45: 4333 1.45 - 1.57: 5929 1.57 - 1.69: 582 1.69 - 1.81: 24 Bond restraints: 12971 Sorted by residual: bond pdb=" N ASP K 194 " pdb=" CA ASP K 194 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.30e-02 5.92e+03 6.27e+00 bond pdb=" N TYR K 196 " pdb=" CA TYR K 196 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.22e+00 bond pdb=" N ALA K 192 " pdb=" CA ALA K 192 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.76e+00 bond pdb=" N GLN K 191 " pdb=" CA GLN K 191 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.56e+00 bond pdb=" P DT J 75 " pdb=" OP2 DT J 75 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 12966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18337 2.04 - 4.08: 397 4.08 - 6.12: 32 6.12 - 8.17: 2 8.17 - 10.21: 3 Bond angle restraints: 18771 Sorted by residual: angle pdb=" C3' DA J 73 " pdb=" O3' DA J 73 " pdb=" P DA J 74 " ideal model delta sigma weight residual 120.20 109.99 10.21 1.50e+00 4.44e-01 4.63e+01 angle pdb=" C3' DG J 72 " pdb=" O3' DG J 72 " pdb=" P DA J 73 " ideal model delta sigma weight residual 120.20 110.32 9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" C3' DA J 71 " pdb=" O3' DA J 71 " pdb=" P DG J 72 " ideal model delta sigma weight residual 120.20 110.39 9.81 1.50e+00 4.44e-01 4.28e+01 angle pdb=" C3' DT J 75 " pdb=" O3' DT J 75 " pdb=" P DC J 76 " ideal model delta sigma weight residual 120.20 112.76 7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C3' DA J 74 " pdb=" O3' DA J 74 " pdb=" P DT J 75 " ideal model delta sigma weight residual 120.20 113.36 6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 18766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 5685 35.79 - 71.58: 1359 71.58 - 107.36: 12 107.36 - 143.15: 0 143.15 - 178.94: 2 Dihedral angle restraints: 7058 sinusoidal: 4799 harmonic: 2259 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 38.94 -178.94 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 42.87 177.13 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2053 0.091 - 0.182: 77 0.182 - 0.274: 0 0.274 - 0.365: 0 0.365 - 0.456: 6 Chirality restraints: 2136 Sorted by residual: chirality pdb=" P DA J 71 " pdb=" OP1 DA J 71 " pdb=" OP2 DA J 71 " pdb=" O5' DA J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" P DT J 75 " pdb=" OP1 DT J 75 " pdb=" OP2 DT J 75 " pdb=" O5' DT J 75 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" P DG J 72 " pdb=" OP1 DG J 72 " pdb=" OP2 DG J 72 " pdb=" O5' DG J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 2133 not shown) Planarity restraints: 1370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 141 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.46e+00 pdb=" N9 DA I 141 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 141 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 141 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 141 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 141 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DA I 141 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA I 141 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA I 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 131 " -0.026 2.00e-02 2.50e+03 1.10e-02 3.35e+00 pdb=" N9 DA I 131 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 131 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 131 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 131 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 131 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.17e+00 pdb=" N9 DA I 39 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.002 2.00e-02 2.50e+03 ... (remaining 1367 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2462 2.80 - 3.32: 9769 3.32 - 3.85: 22246 3.85 - 4.37: 27730 4.37 - 4.90: 38817 Nonbonded interactions: 101024 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.273 3.120 nonbonded pdb=" OE1 GLN E 125 " pdb=" NH1 ARG E 134 " model vdw 2.320 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 181 " model vdw 2.387 3.120 nonbonded pdb=" N VAL C 43 " pdb=" OP1 DA I 113 " model vdw 2.390 3.120 nonbonded pdb=" NH2 ARG C 29 " pdb=" OP1 DC I 123 " model vdw 2.406 3.120 ... (remaining 101019 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 45 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.520 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.008 0.047 12971 Z= 0.333 Angle : 0.726 10.208 18771 Z= 0.444 Chirality : 0.047 0.456 2136 Planarity : 0.004 0.044 1370 Dihedral : 27.266 178.941 5602 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.97 (0.29), residues: 765 helix: 1.58 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 176 HIS 0.002 0.001 HIS E 113 PHE 0.013 0.002 PHE B 61 TYR 0.022 0.002 TYR G 50 ARG 0.010 0.001 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.12203 ( 764) hydrogen bonds : angle 3.94054 ( 1913) covalent geometry : bond 0.00759 (12971) covalent geometry : angle 0.72622 (18771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7726 (pp20) REVERT: G 73 ASN cc_start: 0.8435 (m110) cc_final: 0.8233 (m110) REVERT: H 45 VAL cc_start: 0.8706 (t) cc_final: 0.8469 (m) REVERT: H 73 GLU cc_start: 0.7923 (tp30) cc_final: 0.7574 (tp30) outliers start: 0 outliers final: 1 residues processed: 111 average time/residue: 1.6980 time to fit residues: 200.1246 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN G 112 GLN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057912 restraints weight = 31868.985| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.53 r_work: 0.2883 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12971 Z= 0.173 Angle : 0.580 5.980 18771 Z= 0.352 Chirality : 0.034 0.130 2136 Planarity : 0.004 0.042 1370 Dihedral : 29.986 178.244 4076 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.09 % Allowed : 10.26 % Favored : 88.65 % 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: 1.84 (0.30), residues: 765 helix: 2.21 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 176 HIS 0.003 0.001 HIS H 79 PHE 0.011 0.001 PHE H 67 TYR 0.009 0.001 TYR D 37 ARG 0.006 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 764) hydrogen bonds : angle 2.78492 ( 1913) covalent geometry : bond 0.00370 (12971) covalent geometry : angle 0.57959 (18771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.853 Fit side-chains REVERT: B 59 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8574 (tttp) REVERT: C 15 LYS cc_start: 0.7492 (pttp) cc_final: 0.6997 (pptt) REVERT: C 72 ASP cc_start: 0.7506 (m-30) cc_final: 0.7205 (m-30) REVERT: C 90 ASP cc_start: 0.8459 (t70) cc_final: 0.7974 (t0) REVERT: G 36 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8742 (mmtm) outliers start: 7 outliers final: 0 residues processed: 88 average time/residue: 1.6729 time to fit residues: 156.6321 Evaluate side-chains 68 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.058055 restraints weight = 31863.414| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.47 r_work: 0.2890 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12971 Z= 0.152 Angle : 0.524 7.377 18771 Z= 0.321 Chirality : 0.032 0.125 2136 Planarity : 0.004 0.035 1370 Dihedral : 29.941 177.993 4074 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.33 % Allowed : 10.73 % Favored : 86.94 % 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: 2.49 (0.30), residues: 765 helix: 2.66 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.93 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.008 0.001 PHE B 61 TYR 0.009 0.001 TYR F 51 ARG 0.006 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 764) hydrogen bonds : angle 2.56690 ( 1913) covalent geometry : bond 0.00321 (12971) covalent geometry : angle 0.52450 (18771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.962 Fit side-chains REVERT: C 15 LYS cc_start: 0.7622 (pttp) cc_final: 0.7148 (pptt) REVERT: C 72 ASP cc_start: 0.7220 (m-30) cc_final: 0.6975 (m-30) REVERT: C 90 ASP cc_start: 0.8527 (t70) cc_final: 0.8123 (t0) REVERT: E 76 GLN cc_start: 0.7738 (tt0) cc_final: 0.7535 (tp-100) REVERT: E 131 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8924 (mtp85) REVERT: G 73 ASN cc_start: 0.8417 (t0) cc_final: 0.8212 (t0) outliers start: 15 outliers final: 4 residues processed: 90 average time/residue: 1.6463 time to fit residues: 157.6851 Evaluate side-chains 75 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059249 restraints weight = 31409.184| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.47 r_work: 0.2924 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12971 Z= 0.142 Angle : 0.508 8.384 18771 Z= 0.310 Chirality : 0.031 0.128 2136 Planarity : 0.003 0.033 1370 Dihedral : 29.855 179.489 4074 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.40 % Allowed : 12.91 % Favored : 85.69 % 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 (0.30), residues: 765 helix: 2.84 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.86 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.009 0.001 PHE D 67 TYR 0.007 0.001 TYR F 51 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 764) hydrogen bonds : angle 2.45483 ( 1913) covalent geometry : bond 0.00299 (12971) covalent geometry : angle 0.50845 (18771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.961 Fit side-chains REVERT: C 72 ASP cc_start: 0.6921 (m-30) cc_final: 0.6641 (m-30) REVERT: C 90 ASP cc_start: 0.8431 (t70) cc_final: 0.8011 (t0) REVERT: D 65 ASP cc_start: 0.9321 (t0) cc_final: 0.8909 (t0) REVERT: D 68 GLU cc_start: 0.8145 (tp30) cc_final: 0.7875 (mt-10) REVERT: G 73 ASN cc_start: 0.8479 (t0) cc_final: 0.8236 (t0) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.7229 time to fit residues: 166.8860 Evaluate side-chains 77 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.072158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.054622 restraints weight = 31144.695| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.34 r_work: 0.2806 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12971 Z= 0.207 Angle : 0.558 5.387 18771 Z= 0.337 Chirality : 0.034 0.134 2136 Planarity : 0.004 0.035 1370 Dihedral : 30.150 178.579 4074 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.87 % Allowed : 13.22 % Favored : 84.91 % 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: 2.44 (0.30), residues: 765 helix: 2.62 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS G 82 PHE 0.007 0.001 PHE H 67 TYR 0.011 0.001 TYR F 51 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.05417 ( 764) hydrogen bonds : angle 2.73654 ( 1913) covalent geometry : bond 0.00465 (12971) covalent geometry : angle 0.55806 (18771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.867 Fit side-chains REVERT: C 72 ASP cc_start: 0.7203 (m-30) cc_final: 0.6945 (m-30) REVERT: C 90 ASP cc_start: 0.8613 (t70) cc_final: 0.8295 (t0) REVERT: D 65 ASP cc_start: 0.9391 (t0) cc_final: 0.9141 (t0) REVERT: E 97 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: G 73 ASN cc_start: 0.8725 (t0) cc_final: 0.8430 (t0) outliers start: 12 outliers final: 5 residues processed: 83 average time/residue: 1.6934 time to fit residues: 150.0234 Evaluate side-chains 79 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055109 restraints weight = 31502.055| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.37 r_work: 0.2821 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12971 Z= 0.155 Angle : 0.540 8.657 18771 Z= 0.328 Chirality : 0.033 0.131 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.117 179.263 4074 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.56 % Allowed : 13.37 % Favored : 85.07 % 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: 2.56 (0.30), residues: 765 helix: 2.70 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS G 31 PHE 0.008 0.001 PHE E 78 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 764) hydrogen bonds : angle 2.68860 ( 1913) covalent geometry : bond 0.00330 (12971) covalent geometry : angle 0.54010 (18771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.012 Fit side-chains REVERT: C 72 ASP cc_start: 0.7083 (m-30) cc_final: 0.6792 (m-30) REVERT: C 90 ASP cc_start: 0.8604 (t70) cc_final: 0.8301 (t0) REVERT: D 65 ASP cc_start: 0.9389 (t0) cc_final: 0.9145 (t0) REVERT: E 97 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: G 15 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8394 (mtpp) REVERT: G 73 ASN cc_start: 0.8718 (t0) cc_final: 0.8432 (t0) outliers start: 10 outliers final: 4 residues processed: 81 average time/residue: 1.7687 time to fit residues: 152.1113 Evaluate side-chains 80 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.055010 restraints weight = 31876.763| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.49 r_work: 0.2804 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12971 Z= 0.154 Angle : 0.533 6.519 18771 Z= 0.325 Chirality : 0.033 0.131 2136 Planarity : 0.004 0.034 1370 Dihedral : 30.077 179.330 4074 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 14.46 % Favored : 84.29 % 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: 2.68 (0.30), residues: 765 helix: 2.78 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.83 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.009 0.001 PHE H 67 TYR 0.009 0.001 TYR F 51 ARG 0.003 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 764) hydrogen bonds : angle 2.65552 ( 1913) covalent geometry : bond 0.00329 (12971) covalent geometry : angle 0.53251 (18771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.835 Fit side-chains REVERT: C 72 ASP cc_start: 0.7023 (m-30) cc_final: 0.6708 (m-30) REVERT: C 90 ASP cc_start: 0.8514 (t70) cc_final: 0.8054 (t0) REVERT: D 65 ASP cc_start: 0.9376 (t0) cc_final: 0.9037 (t0) REVERT: E 97 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: G 73 ASN cc_start: 0.8706 (t0) cc_final: 0.8402 (t0) REVERT: K 187 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8448 (tmm-80) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 1.6435 time to fit residues: 134.6290 Evaluate side-chains 81 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 187 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055856 restraints weight = 32031.059| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.50 r_work: 0.2827 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12971 Z= 0.151 Angle : 0.524 10.298 18771 Z= 0.319 Chirality : 0.032 0.128 2136 Planarity : 0.003 0.033 1370 Dihedral : 29.971 179.497 4074 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 14.15 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.30), residues: 765 helix: 2.92 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.001 0.000 HIS G 31 PHE 0.009 0.001 PHE H 67 TYR 0.007 0.001 TYR F 51 ARG 0.003 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 764) hydrogen bonds : angle 2.54236 ( 1913) covalent geometry : bond 0.00322 (12971) covalent geometry : angle 0.52385 (18771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.109 Fit side-chains REVERT: C 72 ASP cc_start: 0.6873 (m-30) cc_final: 0.6564 (m-30) REVERT: D 65 ASP cc_start: 0.9336 (t0) cc_final: 0.8887 (t0) REVERT: E 97 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: G 73 ASN cc_start: 0.8695 (t0) cc_final: 0.8331 (t0) REVERT: K 187 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8435 (tmm-80) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 1.7369 time to fit residues: 147.7136 Evaluate side-chains 81 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain K residue 189 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.056210 restraints weight = 31796.883| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.50 r_work: 0.2838 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12971 Z= 0.148 Angle : 0.522 10.735 18771 Z= 0.318 Chirality : 0.032 0.129 2136 Planarity : 0.003 0.034 1370 Dihedral : 29.947 178.993 4074 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.93 % Allowed : 14.77 % Favored : 84.29 % 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: 2.93 (0.30), residues: 765 helix: 2.96 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE H 67 TYR 0.007 0.001 TYR F 51 ARG 0.002 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 764) hydrogen bonds : angle 2.52385 ( 1913) covalent geometry : bond 0.00314 (12971) covalent geometry : angle 0.52231 (18771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.927 Fit side-chains REVERT: C 72 ASP cc_start: 0.6862 (m-30) cc_final: 0.6503 (m-30) REVERT: D 65 ASP cc_start: 0.9329 (t0) cc_final: 0.9004 (t0) REVERT: E 97 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: G 73 ASN cc_start: 0.8685 (t0) cc_final: 0.8325 (t0) REVERT: K 187 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8379 (tmm-80) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 1.7607 time to fit residues: 138.4217 Evaluate side-chains 78 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 187 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 86 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.053603 restraints weight = 31594.026| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.48 r_work: 0.2762 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12971 Z= 0.229 Angle : 0.569 10.229 18771 Z= 0.342 Chirality : 0.035 0.142 2136 Planarity : 0.004 0.034 1370 Dihedral : 30.114 179.753 4074 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.93 % Allowed : 14.46 % Favored : 84.60 % 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: 2.58 (0.30), residues: 765 helix: 2.72 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.001 HIS H 106 PHE 0.015 0.002 PHE H 67 TYR 0.012 0.001 TYR F 51 ARG 0.005 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 764) hydrogen bonds : angle 2.73087 ( 1913) covalent geometry : bond 0.00522 (12971) covalent geometry : angle 0.56928 (18771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.840 Fit side-chains REVERT: A 59 GLU cc_start: 0.8593 (pm20) cc_final: 0.8373 (pm20) REVERT: C 72 ASP cc_start: 0.7020 (m-30) cc_final: 0.6687 (m-30) REVERT: D 65 ASP cc_start: 0.9388 (t0) cc_final: 0.9058 (t0) REVERT: E 97 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: G 15 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8229 (mtpp) REVERT: K 183 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8307 (mmt90) REVERT: K 187 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8548 (tmm-80) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 1.7088 time to fit residues: 138.1362 Evaluate side-chains 80 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 187 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054091 restraints weight = 31385.835| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.48 r_work: 0.2777 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12971 Z= 0.167 Angle : 0.559 10.055 18771 Z= 0.337 Chirality : 0.033 0.137 2136 Planarity : 0.004 0.033 1370 Dihedral : 30.129 179.808 4074 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.93 % Allowed : 15.09 % Favored : 83.98 % 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: 2.61 (0.30), residues: 765 helix: 2.74 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 176 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE H 67 TYR 0.012 0.001 TYR F 51 ARG 0.004 0.000 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 764) hydrogen bonds : angle 2.71531 ( 1913) covalent geometry : bond 0.00359 (12971) covalent geometry : angle 0.55896 (18771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7249.20 seconds wall clock time: 125 minutes 15.19 seconds (7515.19 seconds total)