Starting phenix.real_space_refine on Sat Sep 28 04:48:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3e_31432/09_2024/7f3e_31432.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 11868 2.51 5 N 3168 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18564 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 5.45, per 1000 atoms: 0.29 Number of scatterers: 18564 At special positions: 0 Unit cell: (102.96, 157.52, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3444 8.00 N 3168 7.00 C 11868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.3 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 18 sheets defined 70.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL E 10 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 11 " --> pdb=" O THR E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 11' Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.741A pdb=" N ASN E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 133 Processing helix chain 'E' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL F 10 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE F 11 " --> pdb=" O THR F 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 7 through 11' Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.741A pdb=" N ASN F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 133 Processing helix chain 'F' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR F 165 " --> pdb=" O GLU F 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP F 166 " --> pdb=" O GLY F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL C 10 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 11 " --> pdb=" O THR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.743A pdb=" N ASN C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 133 Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL D 10 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 11 " --> pdb=" O THR D 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 7 through 11' Processing helix chain 'D' and resid 13 through 20 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.740A pdb=" N ASN D 37 " --> pdb=" O HIS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 114 removed outlier: 3.837A pdb=" N TYR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 133 Processing helix chain 'D' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR D 165 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL A 10 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 11 " --> pdb=" O THR A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 11' Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN A 37 " --> pdb=" O HIS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 114 removed outlier: 3.839A pdb=" N TYR A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL B 10 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 11 " --> pdb=" O THR B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 11' Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN B 37 " --> pdb=" O HIS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.872A pdb=" N PHE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 133 Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.014A pdb=" N VAL B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'H' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL H 10 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE H 11 " --> pdb=" O THR H 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 7 through 11' Processing helix chain 'H' and resid 13 through 20 Processing helix chain 'H' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN H 37 " --> pdb=" O HIS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 114 removed outlier: 3.837A pdb=" N TYR H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 133 Processing helix chain 'H' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TRP H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 190 Processing helix chain 'G' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL G 10 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE G 11 " --> pdb=" O THR G 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 11' Processing helix chain 'G' and resid 13 through 20 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN G 37 " --> pdb=" O HIS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 133 Processing helix chain 'G' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 4.164A pdb=" N THR G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP G 166 " --> pdb=" O GLY G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL J 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE J 11 " --> pdb=" O THR J 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 11' Processing helix chain 'J' and resid 13 through 20 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN J 37 " --> pdb=" O HIS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 56 Processing helix chain 'J' and resid 61 through 68 removed outlier: 3.873A pdb=" N PHE J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 133 Processing helix chain 'J' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP J 166 " --> pdb=" O GLY J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 190 Processing helix chain 'I' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL I 10 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE I 11 " --> pdb=" O THR I 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 11' Processing helix chain 'I' and resid 13 through 20 Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN I 37 " --> pdb=" O HIS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 56 Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.872A pdb=" N PHE I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 114 removed outlier: 3.838A pdb=" N TYR I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 Processing helix chain 'I' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP I 166 " --> pdb=" O GLY I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 190 Processing helix chain 'L' and resid 7 through 11 removed outlier: 3.970A pdb=" N VAL L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 11 " --> pdb=" O THR L 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 7 through 11' Processing helix chain 'L' and resid 13 through 20 Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN L 37 " --> pdb=" O HIS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 56 Processing helix chain 'L' and resid 61 through 68 removed outlier: 3.875A pdb=" N PHE L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 114 removed outlier: 3.840A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 133 Processing helix chain 'L' and resid 139 through 152 removed outlier: 4.013A pdb=" N VAL L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 4.166A pdb=" N THR L 165 " --> pdb=" O GLU L 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP L 166 " --> pdb=" O GLY L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 190 Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.969A pdb=" N VAL K 10 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE K 11 " --> pdb=" O THR K 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 7 through 11' Processing helix chain 'K' and resid 13 through 20 Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.742A pdb=" N ASN K 37 " --> pdb=" O HIS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 68 removed outlier: 3.874A pdb=" N PHE K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 removed outlier: 3.839A pdb=" N TYR K 95 " --> pdb=" O GLU K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 133 Processing helix chain 'K' and resid 139 through 152 removed outlier: 4.012A pdb=" N VAL K 143 " --> pdb=" O SER K 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 removed outlier: 4.165A pdb=" N THR K 165 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP K 166 " --> pdb=" O GLY K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 190 Processing sheet with id=AA1, first strand: chain 'E' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS E 70 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE E 4 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS F 70 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE F 4 " --> pdb=" O TYR F 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS C 70 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE C 4 " --> pdb=" O TYR C 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS D 70 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE D 4 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS A 70 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 4 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS B 70 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 4 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS H 70 " --> pdb=" O PHE H 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE H 4 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.862A pdb=" N LYS G 70 " --> pdb=" O PHE G 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE G 4 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS J 70 " --> pdb=" O PHE J 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE J 4 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 80 through 82 Processing sheet with id=AB6, first strand: chain 'I' and resid 69 through 72 removed outlier: 3.860A pdb=" N LYS I 70 " --> pdb=" O PHE I 42 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE I 4 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS L 70 " --> pdb=" O PHE L 42 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE L 4 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 80 through 82 Processing sheet with id=AB9, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.861A pdb=" N LYS K 70 " --> pdb=" O PHE K 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE K 4 " --> pdb=" O TYR K 43 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6156 1.34 - 1.46: 3204 1.46 - 1.57: 9372 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 18888 Sorted by residual: bond pdb=" CB VAL L 143 " pdb=" CG2 VAL L 143 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG1 ILE I 90 " pdb=" CD1 ILE I 90 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.03e+00 bond pdb=" CB VAL C 143 " pdb=" CG2 VAL C 143 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CG1 ILE K 90 " pdb=" CD1 ILE K 90 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.01e+00 bond pdb=" CB VAL B 143 " pdb=" CG2 VAL B 143 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 ... (remaining 18883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 22717 1.04 - 2.07: 2273 2.07 - 3.11: 278 3.11 - 4.14: 105 4.14 - 5.18: 55 Bond angle restraints: 25428 Sorted by residual: angle pdb=" N THR K 12 " pdb=" CA THR K 12 " pdb=" C THR K 12 " ideal model delta sigma weight residual 114.56 111.72 2.84 1.27e+00 6.20e-01 4.98e+00 angle pdb=" N THR I 12 " pdb=" CA THR I 12 " pdb=" C THR I 12 " ideal model delta sigma weight residual 114.56 111.76 2.80 1.27e+00 6.20e-01 4.87e+00 angle pdb=" N THR L 12 " pdb=" CA THR L 12 " pdb=" C THR L 12 " ideal model delta sigma weight residual 114.56 111.76 2.80 1.27e+00 6.20e-01 4.85e+00 angle pdb=" N GLU I 60 " pdb=" CA GLU I 60 " pdb=" CB GLU I 60 " ideal model delta sigma weight residual 113.65 110.42 3.23 1.47e+00 4.63e-01 4.83e+00 angle pdb=" N THR E 12 " pdb=" CA THR E 12 " pdb=" C THR E 12 " ideal model delta sigma weight residual 114.56 111.77 2.79 1.27e+00 6.20e-01 4.82e+00 ... (remaining 25423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 9739 14.72 - 29.44: 1301 29.44 - 44.16: 312 44.16 - 58.88: 108 58.88 - 73.60: 48 Dihedral angle restraints: 11508 sinusoidal: 4896 harmonic: 6612 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N THR B 12 " pdb=" CA THR B 12 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE J 11 " pdb=" C PHE J 11 " pdb=" N THR J 12 " pdb=" CA THR J 12 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE E 11 " pdb=" C PHE E 11 " pdb=" N THR E 12 " pdb=" CA THR E 12 " ideal model delta harmonic sigma weight residual 180.00 158.67 21.33 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1706 0.033 - 0.066: 747 0.066 - 0.099: 242 0.099 - 0.131: 101 0.131 - 0.164: 36 Chirality restraints: 2832 Sorted by residual: chirality pdb=" CB ILE F 16 " pdb=" CA ILE F 16 " pdb=" CG1 ILE F 16 " pdb=" CG2 ILE F 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE C 16 " pdb=" CA ILE C 16 " pdb=" CG1 ILE C 16 " pdb=" CG2 ILE C 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB ILE G 16 " pdb=" CA ILE G 16 " pdb=" CG1 ILE G 16 " pdb=" CG2 ILE G 16 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 2829 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 73 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO G 74 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 73 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO F 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " 0.038 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " 0.033 5.00e-02 4.00e+02 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3704 2.77 - 3.30: 18450 3.30 - 3.84: 29189 3.84 - 4.37: 34003 4.37 - 4.90: 58577 Nonbonded interactions: 143923 Sorted by model distance: nonbonded pdb=" O GLU K 105 " pdb=" OG1 THR K 108 " model vdw 2.242 3.040 nonbonded pdb=" O GLU B 105 " pdb=" OG1 THR B 108 " model vdw 2.242 3.040 nonbonded pdb=" O GLU D 105 " pdb=" OG1 THR D 108 " model vdw 2.243 3.040 nonbonded pdb=" O GLU J 105 " pdb=" OG1 THR J 108 " model vdw 2.243 3.040 nonbonded pdb=" O GLU A 105 " pdb=" OG1 THR A 108 " model vdw 2.243 3.040 ... (remaining 143918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.690 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 35.500 Find NCS groups from input model: 0.890 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 0.040 18888 Z= 0.330 Angle : 0.709 5.179 25428 Z= 0.426 Chirality : 0.045 0.164 2832 Planarity : 0.005 0.059 3252 Dihedral : 15.180 73.599 7212 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.41 (0.17), residues: 2208 helix: 0.86 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -2.50 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 166 HIS 0.002 0.001 HIS J 33 PHE 0.014 0.002 PHE A 31 TYR 0.012 0.002 TYR B 128 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASN cc_start: 0.5555 (t0) cc_final: 0.5293 (m-40) REVERT: C 51 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6167 (mm-30) REVERT: D 55 ILE cc_start: 0.7123 (mt) cc_final: 0.6551 (mt) REVERT: D 160 ASP cc_start: 0.7527 (t70) cc_final: 0.6261 (m-30) REVERT: J 13 ASN cc_start: 0.5631 (t0) cc_final: 0.5373 (m-40) REVERT: J 51 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6178 (mm-30) REVERT: J 98 ASN cc_start: 0.7757 (m-40) cc_final: 0.7534 (m-40) REVERT: I 55 ILE cc_start: 0.7212 (mt) cc_final: 0.6674 (mt) REVERT: I 160 ASP cc_start: 0.7614 (t70) cc_final: 0.6345 (m-30) REVERT: L 160 ASP cc_start: 0.5787 (t70) cc_final: 0.5510 (m-30) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3142 time to fit residues: 210.4108 Evaluate side-chains 255 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18888 Z= 0.214 Angle : 0.604 6.341 25428 Z= 0.330 Chirality : 0.044 0.138 2832 Planarity : 0.005 0.050 3252 Dihedral : 4.533 21.501 2520 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.95 % Allowed : 10.63 % Favored : 88.42 % 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: -0.36 (0.17), residues: 2208 helix: 0.87 (0.13), residues: 1500 sheet: -1.72 (0.47), residues: 120 loop : -2.82 (0.20), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 166 HIS 0.003 0.001 HIS J 190 PHE 0.018 0.002 PHE A 77 TYR 0.026 0.001 TYR K 87 ARG 0.006 0.001 ARG H 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 293 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 7 ASP cc_start: 0.6519 (t70) cc_final: 0.6078 (t0) REVERT: F 56 MET cc_start: 0.7419 (tmm) cc_final: 0.7113 (tmm) REVERT: C 67 MET cc_start: 0.4800 (mmm) cc_final: 0.4558 (mpp) REVERT: D 51 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: G 56 MET cc_start: 0.7397 (tmm) cc_final: 0.7094 (tmm) REVERT: J 98 ASN cc_start: 0.7815 (m-40) cc_final: 0.7515 (m110) REVERT: K 1 MET cc_start: 0.1509 (tpt) cc_final: 0.1034 (tpt) outliers start: 19 outliers final: 17 residues processed: 303 average time/residue: 0.3155 time to fit residues: 143.9598 Evaluate side-chains 249 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN C 190 HIS ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN J 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18888 Z= 0.186 Angle : 0.555 6.531 25428 Z= 0.301 Chirality : 0.043 0.135 2832 Planarity : 0.004 0.044 3252 Dihedral : 4.272 20.434 2520 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.35 % Allowed : 15.17 % Favored : 82.49 % 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: -0.11 (0.18), residues: 2208 helix: 1.11 (0.14), residues: 1488 sheet: -1.71 (0.43), residues: 120 loop : -2.78 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 166 HIS 0.009 0.001 HIS F 33 PHE 0.024 0.001 PHE J 11 TYR 0.015 0.001 TYR B 87 ARG 0.006 0.000 ARG H 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 255 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.4240 (p90) REVERT: D 51 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: D 64 GLU cc_start: 0.5411 (mm-30) cc_final: 0.5186 (mm-30) REVERT: D 178 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6661 (mppt) REVERT: A 80 THR cc_start: 0.7392 (p) cc_final: 0.6902 (t) REVERT: B 52 MET cc_start: 0.7636 (tmm) cc_final: 0.7115 (ttp) REVERT: B 153 ASP cc_start: 0.7317 (m-30) cc_final: 0.7095 (m-30) REVERT: G 133 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8045 (mtp85) REVERT: J 98 ASN cc_start: 0.7768 (m-40) cc_final: 0.7466 (m-40) REVERT: L 80 THR cc_start: 0.7377 (p) cc_final: 0.6904 (t) outliers start: 47 outliers final: 29 residues processed: 287 average time/residue: 0.2982 time to fit residues: 131.1164 Evaluate side-chains 256 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 0.4980 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN D 179 ASN A 179 ASN J 179 ASN L 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18888 Z= 0.407 Angle : 0.708 6.743 25428 Z= 0.379 Chirality : 0.048 0.165 2832 Planarity : 0.005 0.039 3252 Dihedral : 5.027 25.368 2520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.14 % Allowed : 17.66 % Favored : 78.19 % 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: -0.46 (0.18), residues: 2208 helix: 0.75 (0.13), residues: 1488 sheet: -1.57 (0.55), residues: 120 loop : -2.72 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 62 HIS 0.008 0.001 HIS F 33 PHE 0.042 0.003 PHE H 31 TYR 0.026 0.002 TYR K 87 ARG 0.006 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 239 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4313 (p90) REVERT: C 67 MET cc_start: 0.4866 (mtt) cc_final: 0.4535 (mpp) REVERT: C 151 GLU cc_start: 0.6368 (pt0) cc_final: 0.5947 (tt0) REVERT: D 51 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: D 64 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5790 (mm-30) REVERT: D 178 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6940 (mppt) REVERT: D 187 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6212 (tt) REVERT: A 70 LYS cc_start: 0.6752 (mppt) cc_final: 0.6538 (mmtm) REVERT: A 80 THR cc_start: 0.7558 (p) cc_final: 0.7102 (t) REVERT: B 52 MET cc_start: 0.7751 (tmm) cc_final: 0.6524 (ttt) REVERT: J 98 ASN cc_start: 0.7874 (m-40) cc_final: 0.7656 (m-40) REVERT: L 80 THR cc_start: 0.7554 (p) cc_final: 0.7147 (t) outliers start: 83 outliers final: 46 residues processed: 301 average time/residue: 0.2890 time to fit residues: 134.6216 Evaluate side-chains 267 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.0020 chunk 118 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 178 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 0.0050 chunk 52 optimal weight: 0.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN A 179 ASN J 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18888 Z= 0.156 Angle : 0.527 6.510 25428 Z= 0.288 Chirality : 0.042 0.127 2832 Planarity : 0.004 0.037 3252 Dihedral : 4.213 22.083 2520 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.99 % Allowed : 19.51 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.18), residues: 2208 helix: 1.07 (0.14), residues: 1488 sheet: -1.99 (0.37), residues: 120 loop : -2.67 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 62 HIS 0.009 0.001 HIS F 33 PHE 0.021 0.001 PHE J 11 TYR 0.022 0.001 TYR K 87 ARG 0.005 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 248 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4620 (OUTLIER) cc_final: 0.4179 (p90) REVERT: C 67 MET cc_start: 0.5058 (mtt) cc_final: 0.4642 (mpp) REVERT: C 151 GLU cc_start: 0.6237 (pt0) cc_final: 0.5799 (tt0) REVERT: D 178 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7091 (mppt) REVERT: A 80 THR cc_start: 0.7543 (p) cc_final: 0.7163 (t) REVERT: J 98 ASN cc_start: 0.7810 (m-40) cc_final: 0.7561 (m-40) REVERT: L 70 LYS cc_start: 0.6823 (mppt) cc_final: 0.6539 (mmtm) REVERT: L 80 THR cc_start: 0.7583 (p) cc_final: 0.7109 (t) outliers start: 60 outliers final: 40 residues processed: 291 average time/residue: 0.3225 time to fit residues: 145.9217 Evaluate side-chains 261 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 173 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN J 179 ASN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18888 Z= 0.165 Angle : 0.520 6.540 25428 Z= 0.283 Chirality : 0.042 0.124 2832 Planarity : 0.003 0.038 3252 Dihedral : 4.150 22.082 2520 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.94 % Allowed : 19.81 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.18), residues: 2208 helix: 1.12 (0.14), residues: 1488 sheet: -2.09 (0.35), residues: 120 loop : -2.51 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 62 HIS 0.009 0.001 HIS G 33 PHE 0.021 0.001 PHE D 180 TYR 0.030 0.001 TYR K 87 ARG 0.006 0.000 ARG H 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 236 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.4249 (p90) REVERT: C 151 GLU cc_start: 0.6214 (pt0) cc_final: 0.5801 (tt0) REVERT: D 51 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: D 120 LEU cc_start: 0.6805 (mt) cc_final: 0.6539 (mt) REVERT: A 80 THR cc_start: 0.7589 (p) cc_final: 0.7193 (t) REVERT: J 98 ASN cc_start: 0.7768 (m-40) cc_final: 0.7565 (m-40) REVERT: L 80 THR cc_start: 0.7466 (p) cc_final: 0.7052 (t) outliers start: 59 outliers final: 39 residues processed: 280 average time/residue: 0.3054 time to fit residues: 133.1041 Evaluate side-chains 256 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 215 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN J 179 ASN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18888 Z= 0.223 Angle : 0.559 6.791 25428 Z= 0.302 Chirality : 0.043 0.135 2832 Planarity : 0.004 0.041 3252 Dihedral : 4.325 21.597 2520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.39 % Allowed : 20.56 % Favored : 76.05 % 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: -0.08 (0.18), residues: 2208 helix: 1.07 (0.14), residues: 1488 sheet: -2.21 (0.35), residues: 120 loop : -2.46 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 62 HIS 0.009 0.001 HIS F 33 PHE 0.025 0.002 PHE D 180 TYR 0.029 0.001 TYR K 87 ARG 0.008 0.000 ARG G 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 212 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.4115 (p90) REVERT: F 51 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 151 GLU cc_start: 0.6279 (pt0) cc_final: 0.5854 (tt0) REVERT: D 51 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: D 120 LEU cc_start: 0.6796 (mt) cc_final: 0.6539 (mt) REVERT: A 80 THR cc_start: 0.7675 (p) cc_final: 0.7226 (t) REVERT: G 51 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7164 (mm-30) REVERT: L 20 PHE cc_start: 0.3981 (OUTLIER) cc_final: 0.3715 (m-80) REVERT: L 80 THR cc_start: 0.7347 (p) cc_final: 0.6993 (t) outliers start: 68 outliers final: 49 residues processed: 261 average time/residue: 0.2850 time to fit residues: 117.3925 Evaluate side-chains 257 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 205 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18888 Z= 0.171 Angle : 0.527 8.599 25428 Z= 0.285 Chirality : 0.042 0.133 2832 Planarity : 0.003 0.037 3252 Dihedral : 4.166 22.580 2520 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.54 % Allowed : 20.76 % Favored : 75.70 % 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: -0.02 (0.18), residues: 2208 helix: 1.10 (0.14), residues: 1488 sheet: -2.13 (0.35), residues: 120 loop : -2.37 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 166 HIS 0.009 0.001 HIS F 33 PHE 0.027 0.001 PHE D 180 TYR 0.025 0.001 TYR K 87 ARG 0.007 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 220 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4514 (OUTLIER) cc_final: 0.4150 (p90) REVERT: F 51 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7109 (mm-30) REVERT: C 151 GLU cc_start: 0.6214 (pt0) cc_final: 0.5831 (tt0) REVERT: D 51 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: D 120 LEU cc_start: 0.6761 (mt) cc_final: 0.6523 (mt) REVERT: A 80 THR cc_start: 0.7627 (p) cc_final: 0.7137 (t) REVERT: B 126 GLU cc_start: 0.5298 (mm-30) cc_final: 0.4397 (pt0) REVERT: B 180 PHE cc_start: 0.2091 (t80) cc_final: 0.1452 (t80) REVERT: L 20 PHE cc_start: 0.4015 (OUTLIER) cc_final: 0.3759 (m-80) REVERT: L 80 THR cc_start: 0.7339 (p) cc_final: 0.6971 (t) outliers start: 71 outliers final: 48 residues processed: 272 average time/residue: 0.2832 time to fit residues: 119.1429 Evaluate side-chains 253 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 202 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 56 MET Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 0.031 18888 Z= 0.203 Angle : 0.556 7.294 25428 Z= 0.302 Chirality : 0.042 0.133 2832 Planarity : 0.004 0.037 3252 Dihedral : 4.279 22.358 2520 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.09 % Allowed : 21.41 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.18), residues: 2208 helix: 1.10 (0.14), residues: 1488 sheet: -2.23 (0.35), residues: 120 loop : -2.34 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 62 HIS 0.009 0.001 HIS F 33 PHE 0.021 0.001 PHE J 11 TYR 0.024 0.001 TYR K 87 ARG 0.007 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4097 (p90) REVERT: F 51 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 151 GLU cc_start: 0.6343 (pt0) cc_final: 0.5871 (tt0) REVERT: D 51 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: D 120 LEU cc_start: 0.6764 (mt) cc_final: 0.6538 (mt) REVERT: A 80 THR cc_start: 0.7578 (p) cc_final: 0.7146 (t) REVERT: H 33 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5900 (p-80) REVERT: J 67 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.3980 (mtt) REVERT: L 20 PHE cc_start: 0.4086 (OUTLIER) cc_final: 0.3861 (m-80) REVERT: L 73 SER cc_start: 0.7322 (t) cc_final: 0.6866 (p) REVERT: L 80 THR cc_start: 0.7387 (p) cc_final: 0.6999 (t) outliers start: 62 outliers final: 51 residues processed: 250 average time/residue: 0.2689 time to fit residues: 106.9210 Evaluate side-chains 254 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 198 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 33 HIS Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18888 Z= 0.271 Angle : 0.603 7.421 25428 Z= 0.326 Chirality : 0.044 0.141 2832 Planarity : 0.004 0.039 3252 Dihedral : 4.544 23.792 2520 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.04 % Allowed : 21.81 % Favored : 75.15 % 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: -0.16 (0.18), residues: 2208 helix: 0.99 (0.14), residues: 1488 sheet: -2.43 (0.34), residues: 120 loop : -2.38 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 62 HIS 0.009 0.001 HIS F 33 PHE 0.023 0.002 PHE J 11 TYR 0.025 0.002 TYR K 87 ARG 0.008 0.000 ARG E 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 201 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: E 11 PHE cc_start: 0.4761 (OUTLIER) cc_final: 0.4088 (p90) REVERT: C 151 GLU cc_start: 0.6425 (pt0) cc_final: 0.5951 (tt0) REVERT: D 51 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 80 THR cc_start: 0.7681 (p) cc_final: 0.7227 (t) REVERT: H 33 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.6089 (p-80) REVERT: J 67 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3967 (mtt) REVERT: L 73 SER cc_start: 0.7490 (t) cc_final: 0.6923 (p) REVERT: L 80 THR cc_start: 0.7412 (p) cc_final: 0.7022 (t) REVERT: L 169 LYS cc_start: 0.7894 (tptp) cc_final: 0.7512 (tttm) outliers start: 61 outliers final: 50 residues processed: 245 average time/residue: 0.2664 time to fit residues: 105.0785 Evaluate side-chains 248 residues out of total 2004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 33 HIS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.239627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.226950 restraints weight = 22014.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207150 restraints weight = 31222.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.207315 restraints weight = 30859.039| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18888 Z= 0.174 Angle : 0.548 8.246 25428 Z= 0.297 Chirality : 0.042 0.131 2832 Planarity : 0.003 0.038 3252 Dihedral : 4.253 25.127 2520 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.64 % Allowed : 22.50 % Favored : 74.85 % 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: -0.02 (0.18), residues: 2208 helix: 1.09 (0.14), residues: 1488 sheet: -2.30 (0.34), residues: 120 loop : -2.30 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 62 HIS 0.010 0.001 HIS F 33 PHE 0.015 0.001 PHE J 11 TYR 0.022 0.001 TYR K 87 ARG 0.007 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3482.34 seconds wall clock time: 63 minutes 31.08 seconds (3811.08 seconds total)