Starting phenix.real_space_refine on Wed Sep 17 23:48:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mr7_48554/09_2025/9mr7_48554.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 73 5.16 5 C 7908 2.51 5 N 2116 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12463 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1732 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "C" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1528 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain: "D" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 838 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 98} Chain: "E" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 838 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 98} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 791 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 95} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 897 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 804 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "L" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Time building chain proxies: 2.84, per 1000 atoms: 0.23 Number of scatterers: 12463 At special positions: 0 Unit cell: (88, 135.3, 173.8, 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 73 16.00 O 2366 8.00 N 2116 7.00 C 7908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 199 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 41 " distance=2.03 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 372.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 23 sheets defined 15.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.762A pdb=" N VAL A 18 " --> pdb=" O PRO A 14 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 removed outlier: 3.642A pdb=" N HIS A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 removed outlier: 3.752A pdb=" N GLN A 42 " --> pdb=" O ARG A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.895A pdb=" N THR A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.954A pdb=" N GLY A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.193A pdb=" N GLN A 205 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.835A pdb=" N GLN B 12 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 38 through 46 removed outlier: 3.722A pdb=" N GLN B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.999A pdb=" N GLY B 68 " --> pdb=" O GLY B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.678A pdb=" N LYS B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.613A pdb=" N LEU C 12 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 4.156A pdb=" N GLY C 21 " --> pdb=" O GLY C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 38 through 46 removed outlier: 3.526A pdb=" N ARG C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.620A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 159 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.514A pdb=" N ALA E 46 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS E 47 " --> pdb=" O PRO E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 47' Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.580A pdb=" N VAL E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET E 67 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 66 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.583A pdb=" N ALA G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.881A pdb=" N SER H 31 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.819A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.155A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.722A pdb=" N LYS J 64 " --> pdb=" O SER J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.623A pdb=" N THR J 87 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.518A pdb=" N LYS A 9 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP A 11 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 87 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE A 84 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 148 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY A 86 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 146 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 88 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL A 144 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 90 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 144 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.754A pdb=" N PHE A 23 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.714A pdb=" N ILE A 198 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.909A pdb=" N GLY B 60 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AA8, first strand: chain 'B' and resid 101 through 102 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 102 current: chain 'B' and resid 119 through 125 removed outlier: 4.153A pdb=" N ILE B 131 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG B 125 " --> pdb=" O PRO B 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 128 through 135 current: chain 'B' and resid 183 through 191 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 191 current: chain 'C' and resid 119 through 125 removed outlier: 6.521A pdb=" N LEU C 119 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS C 134 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 121 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY C 132 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE C 123 " --> pdb=" O VAL C 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 128 through 135 current: chain 'C' and resid 183 through 191 removed outlier: 10.573A pdb=" N THR C 187 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL D 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D 33 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL D 16 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N CYS D 31 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N MET D 18 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU D 29 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ARG D 27 " --> pdb=" O PRO D 20 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 48 through 55 current: chain 'D' and resid 92 through 102 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 102 current: chain 'E' and resid 27 through 36 removed outlier: 3.502A pdb=" N MET E 28 " --> pdb=" O LYS E 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 48 through 55 current: chain 'E' and resid 92 through 102 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 102 current: chain 'F' and resid 23 through 31 removed outlier: 3.987A pdb=" N VAL F 38 " --> pdb=" O ALA F 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 43 current: chain 'F' and resid 84 through 91 Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AB1, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.838A pdb=" N SER G 7 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.221A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.756A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.534A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.767A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.641A pdb=" N THR I 5 " --> pdb=" O ARG I 24 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.538A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.655A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU J 80 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100C through 100D Processing sheet with id=AC2, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.891A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 13 current: chain 'K' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 44 through 48 current: chain 'K' and resid 97 through 98 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN L 3 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU L 18 " --> pdb=" O MET L 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET L 82 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE L 77 " --> pdb=" O ASP L 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 46 through 51 removed outlier: 3.548A pdb=" N GLU L 58 " --> pdb=" O PHE L 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 57 through 59 current: chain 'L' and resid 100A through 103 292 hydrogen bonds defined for protein. 777 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: 1.66 Time building geometry restraints manager: 0.98 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: 3974 1.34 - 1.46: 3281 1.46 - 1.58: 5402 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 12765 Sorted by residual: bond pdb=" C GLN I 79 " pdb=" N PRO I 80 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.19e-02 7.06e+03 6.10e+00 bond pdb=" C ALA L 40 " pdb=" N PRO L 41 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.25e+00 bond pdb=" CA THR G 69 " pdb=" C THR G 69 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.49e-02 4.50e+03 1.83e+00 bond pdb=" CB TRP G 91 " pdb=" CG TRP G 91 " ideal model delta sigma weight residual 1.498 1.533 -0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CA THR G 69 " pdb=" CB THR G 69 " ideal model delta sigma weight residual 1.533 1.551 -0.017 1.66e-02 3.63e+03 1.06e+00 ... (remaining 12760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 16849 1.80 - 3.61: 415 3.61 - 5.41: 58 5.41 - 7.22: 6 7.22 - 9.02: 3 Bond angle restraints: 17331 Sorted by residual: angle pdb=" CA TRP G 91 " pdb=" CB TRP G 91 " pdb=" CG TRP G 91 " ideal model delta sigma weight residual 113.60 119.06 -5.46 1.90e+00 2.77e-01 8.26e+00 angle pdb=" C ALA H 99 " pdb=" CA ALA H 99 " pdb=" CB ALA H 99 " ideal model delta sigma weight residual 110.42 115.87 -5.45 1.99e+00 2.53e-01 7.49e+00 angle pdb=" OG1 THR G 69 " pdb=" CB THR G 69 " pdb=" CG2 THR G 69 " ideal model delta sigma weight residual 109.30 103.86 5.44 2.00e+00 2.50e-01 7.40e+00 angle pdb=" CB MET C 155 " pdb=" CG MET C 155 " pdb=" SD MET C 155 " ideal model delta sigma weight residual 112.70 120.49 -7.79 3.00e+00 1.11e-01 6.74e+00 angle pdb=" CA LEU L 45 " pdb=" CB LEU L 45 " pdb=" CG LEU L 45 " ideal model delta sigma weight residual 116.30 125.32 -9.02 3.50e+00 8.16e-02 6.64e+00 ... (remaining 17326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6994 17.65 - 35.29: 476 35.29 - 52.93: 67 52.93 - 70.58: 25 70.58 - 88.22: 5 Dihedral angle restraints: 7567 sinusoidal: 2955 harmonic: 4612 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -144.16 58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS B 192 " pdb=" SG CYS B 192 " pdb=" SG CYS B 199 " pdb=" CB CYS B 199 " ideal model delta sinusoidal sigma weight residual -86.00 -133.57 47.57 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS E 103 " pdb=" SG CYS E 103 " pdb=" SG CYS E 109 " pdb=" CB CYS E 109 " ideal model delta sinusoidal sigma weight residual 93.00 136.71 -43.71 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 7564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1655 0.073 - 0.147: 229 0.147 - 0.220: 11 0.220 - 0.294: 0 0.294 - 0.367: 1 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB ILE A 136 " pdb=" CA ILE A 136 " pdb=" CG1 ILE A 136 " pdb=" CG2 ILE A 136 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL C 163 " pdb=" N VAL C 163 " pdb=" C VAL C 163 " pdb=" CB VAL C 163 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ILE I 48 " pdb=" N ILE I 48 " pdb=" C ILE I 48 " pdb=" CB ILE I 48 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1893 not shown) Planarity restraints: 2214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 16 " 0.250 9.50e-02 1.11e+02 1.13e-01 1.02e+01 pdb=" NE ARG L 16 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG L 16 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG L 16 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG L 16 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 38 " 0.251 9.50e-02 1.11e+02 1.13e-01 1.01e+01 pdb=" NE ARG L 38 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG L 38 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG L 38 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG L 38 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 193 " 0.238 9.50e-02 1.11e+02 1.08e-01 9.11e+00 pdb=" NE ARG A 193 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 193 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 193 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 193 " 0.000 2.00e-02 2.50e+03 ... (remaining 2211 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2083 2.77 - 3.30: 10647 3.30 - 3.84: 18931 3.84 - 4.37: 20770 4.37 - 4.90: 38632 Nonbonded interactions: 91063 Sorted by model distance: nonbonded pdb=" OE1 GLN B 42 " pdb=" OG1 THR K 93 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 104 " pdb=" O ARG A 117 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU B 182 " pdb=" OH TYR B 184 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG C 36 " pdb=" OH TYR I 32 " model vdw 2.294 3.120 nonbonded pdb=" OE2 GLU C 171 " pdb=" OH TYR C 173 " model vdw 2.301 3.040 ... (remaining 91058 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 'D' selection = chain 'E' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12784 Z= 0.143 Angle : 0.669 9.020 17369 Z= 0.350 Chirality : 0.049 0.367 1896 Planarity : 0.008 0.113 2214 Dihedral : 12.261 88.225 4596 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.22 % Allowed : 1.93 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.20), residues: 1579 helix: 0.51 (0.40), residues: 166 sheet: -0.32 (0.22), residues: 551 loop : -0.88 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG L 16 TYR 0.018 0.002 TYR L 33 PHE 0.017 0.002 PHE K 87 TRP 0.013 0.001 TRP L 47 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00304 (12765) covalent geometry : angle 0.66704 (17331) SS BOND : bond 0.00476 ( 19) SS BOND : angle 1.34572 ( 38) hydrogen bonds : bond 0.26409 ( 292) hydrogen bonds : angle 8.18976 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 154 average time/residue: 0.1506 time to fit residues: 30.4792 Evaluate side-chains 72 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0270 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 7.9990 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN J 53 ASN K 38 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.032798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.028269 restraints weight = 133230.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.029073 restraints weight = 66721.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.029609 restraints weight = 42839.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.029980 restraints weight = 31809.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.030227 restraints weight = 25645.550| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12784 Z= 0.126 Angle : 0.571 8.042 17369 Z= 0.298 Chirality : 0.043 0.207 1896 Planarity : 0.005 0.045 2214 Dihedral : 4.233 28.857 1797 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.11 % Allowed : 6.39 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.20), residues: 1579 helix: 0.97 (0.42), residues: 169 sheet: -0.10 (0.22), residues: 545 loop : -0.76 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 38 TYR 0.015 0.001 TYR L 33 PHE 0.008 0.001 PHE I 87 TRP 0.007 0.001 TRP J 47 HIS 0.003 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00286 (12765) covalent geometry : angle 0.56973 (17331) SS BOND : bond 0.00554 ( 19) SS BOND : angle 0.92656 ( 38) hydrogen bonds : bond 0.04701 ( 292) hydrogen bonds : angle 6.25460 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.9152 (ttm) cc_final: 0.8883 (ttp) REVERT: C 158 MET cc_start: 0.8849 (tpp) cc_final: 0.8400 (tpp) REVERT: C 170 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7829 (tm-30) REVERT: K 103 LYS cc_start: 0.9127 (tppt) cc_final: 0.8912 (tptp) REVERT: L 18 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8867 (tt) REVERT: L 72 ASP cc_start: 0.8873 (t0) cc_final: 0.7258 (t70) REVERT: L 75 LYS cc_start: 0.9573 (mtpt) cc_final: 0.9238 (mtmm) REVERT: L 77 ILE cc_start: 0.9322 (mt) cc_final: 0.9065 (mm) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 0.1076 time to fit residues: 13.2910 Evaluate side-chains 69 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 96 optimal weight: 0.0670 chunk 120 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.032267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.027844 restraints weight = 135496.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.028630 restraints weight = 66873.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.029172 restraints weight = 42868.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.029532 restraints weight = 31692.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.029791 restraints weight = 25506.048| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12784 Z= 0.113 Angle : 0.520 6.435 17369 Z= 0.269 Chirality : 0.042 0.180 1896 Planarity : 0.004 0.040 2214 Dihedral : 4.112 28.453 1797 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.04 % Allowed : 7.28 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.21), residues: 1579 helix: 1.11 (0.42), residues: 164 sheet: 0.04 (0.22), residues: 536 loop : -0.56 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 38 TYR 0.010 0.001 TYR I 49 PHE 0.007 0.001 PHE G 98 TRP 0.008 0.001 TRP J 47 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00255 (12765) covalent geometry : angle 0.51906 (17331) SS BOND : bond 0.00382 ( 19) SS BOND : angle 0.75122 ( 38) hydrogen bonds : bond 0.03610 ( 292) hydrogen bonds : angle 5.56868 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 158 MET cc_start: 0.8859 (tpp) cc_final: 0.8438 (tpp) REVERT: E 11 MET cc_start: 0.8165 (mmt) cc_final: 0.7648 (mmm) REVERT: J 82 MET cc_start: 0.8867 (mtp) cc_final: 0.8473 (mtp) REVERT: K 103 LYS cc_start: 0.9139 (tppt) cc_final: 0.8867 (tptm) REVERT: L 18 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8826 (tt) outliers start: 14 outliers final: 7 residues processed: 77 average time/residue: 0.1165 time to fit residues: 13.2570 Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.031323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.026937 restraints weight = 138746.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.027696 restraints weight = 69023.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.028219 restraints weight = 44445.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.028561 restraints weight = 33006.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.028797 restraints weight = 26816.470| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12784 Z= 0.172 Angle : 0.550 5.909 17369 Z= 0.286 Chirality : 0.042 0.159 1896 Planarity : 0.004 0.042 2214 Dihedral : 4.353 28.574 1797 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.49 % Allowed : 8.99 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1579 helix: 1.15 (0.42), residues: 165 sheet: 0.10 (0.22), residues: 547 loop : -0.51 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 36 TYR 0.017 0.001 TYR L 79 PHE 0.012 0.001 PHE I 36 TRP 0.008 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00395 (12765) covalent geometry : angle 0.54894 (17331) SS BOND : bond 0.00444 ( 19) SS BOND : angle 0.89176 ( 38) hydrogen bonds : bond 0.03613 ( 292) hydrogen bonds : angle 5.41696 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8444 (mmm) cc_final: 0.7865 (mmm) REVERT: C 158 MET cc_start: 0.8953 (tpp) cc_final: 0.8348 (tpp) REVERT: D 18 MET cc_start: 0.8225 (ttt) cc_final: 0.8015 (mtp) REVERT: E 11 MET cc_start: 0.8497 (mmt) cc_final: 0.7970 (mmm) outliers start: 20 outliers final: 14 residues processed: 75 average time/residue: 0.1113 time to fit residues: 12.5721 Evaluate side-chains 70 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.2980 chunk 92 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.032009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027649 restraints weight = 136807.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.028439 restraints weight = 67441.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.028974 restraints weight = 42944.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.029331 restraints weight = 31608.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.029577 restraints weight = 25492.869| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12784 Z= 0.083 Angle : 0.477 7.493 17369 Z= 0.245 Chirality : 0.041 0.159 1896 Planarity : 0.004 0.039 2214 Dihedral : 3.969 28.173 1797 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.89 % Allowed : 9.44 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.21), residues: 1579 helix: 1.27 (0.41), residues: 165 sheet: 0.19 (0.22), residues: 543 loop : -0.44 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.008 0.001 TYR A 8 PHE 0.006 0.001 PHE D 52 TRP 0.010 0.001 TRP F 52 HIS 0.002 0.000 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00189 (12765) covalent geometry : angle 0.47701 (17331) SS BOND : bond 0.00323 ( 19) SS BOND : angle 0.64386 ( 38) hydrogen bonds : bond 0.02928 ( 292) hydrogen bonds : angle 5.00142 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8448 (mmm) cc_final: 0.7814 (mmm) REVERT: B 152 MET cc_start: 0.9070 (mmm) cc_final: 0.8810 (mmm) REVERT: C 158 MET cc_start: 0.8782 (tpp) cc_final: 0.8390 (tpp) REVERT: D 57 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8623 (mmtm) REVERT: E 11 MET cc_start: 0.8553 (mmt) cc_final: 0.8155 (mmm) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.1182 time to fit residues: 12.4311 Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 0.0370 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS F 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.030713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.026343 restraints weight = 141542.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.027083 restraints weight = 70808.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.027597 restraints weight = 45837.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.027937 restraints weight = 34224.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028167 restraints weight = 27846.723| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12784 Z= 0.216 Angle : 0.579 6.840 17369 Z= 0.301 Chirality : 0.042 0.151 1896 Planarity : 0.004 0.043 2214 Dihedral : 4.480 29.408 1797 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.34 % Allowed : 9.88 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1579 helix: 0.94 (0.42), residues: 173 sheet: 0.06 (0.22), residues: 550 loop : -0.46 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.020 0.002 TYR J 98 PHE 0.015 0.001 PHE I 36 TRP 0.008 0.001 TRP K 35 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00490 (12765) covalent geometry : angle 0.57766 (17331) SS BOND : bond 0.00413 ( 19) SS BOND : angle 0.94698 ( 38) hydrogen bonds : bond 0.03625 ( 292) hydrogen bonds : angle 5.33255 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.475 Fit side-chains REVERT: A 194 MET cc_start: 0.8439 (mmm) cc_final: 0.8019 (mmm) REVERT: A 202 MET cc_start: 0.9361 (ttm) cc_final: 0.9005 (ttp) REVERT: B 35 LEU cc_start: 0.8964 (tp) cc_final: 0.8525 (tp) REVERT: B 152 MET cc_start: 0.9133 (mmm) cc_final: 0.8898 (mmm) REVERT: C 158 MET cc_start: 0.9002 (tpp) cc_final: 0.8632 (tpp) REVERT: E 11 MET cc_start: 0.8538 (mmt) cc_final: 0.8075 (mmm) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.0967 time to fit residues: 10.7656 Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.031209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.026866 restraints weight = 137275.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.027629 restraints weight = 68467.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.028152 restraints weight = 43920.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.028498 restraints weight = 32584.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.028740 restraints weight = 26344.152| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12784 Z= 0.101 Angle : 0.506 7.200 17369 Z= 0.260 Chirality : 0.042 0.166 1896 Planarity : 0.004 0.039 2214 Dihedral : 4.205 29.096 1797 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 10.55 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1579 helix: 1.15 (0.41), residues: 172 sheet: 0.14 (0.22), residues: 558 loop : -0.41 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 36 TYR 0.011 0.001 TYR L 79 PHE 0.006 0.001 PHE D 52 TRP 0.009 0.001 TRP J 47 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00237 (12765) covalent geometry : angle 0.50491 (17331) SS BOND : bond 0.00334 ( 19) SS BOND : angle 0.73642 ( 38) hydrogen bonds : bond 0.03066 ( 292) hydrogen bonds : angle 5.06311 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.421 Fit side-chains REVERT: A 194 MET cc_start: 0.8390 (mmm) cc_final: 0.7949 (mmm) REVERT: A 202 MET cc_start: 0.9376 (ttm) cc_final: 0.9023 (ttp) REVERT: B 152 MET cc_start: 0.9131 (mmm) cc_final: 0.8896 (mmm) REVERT: C 158 MET cc_start: 0.8903 (tpp) cc_final: 0.8413 (tpp) REVERT: E 11 MET cc_start: 0.8536 (mmt) cc_final: 0.8140 (mmm) REVERT: E 18 MET cc_start: 0.8327 (mtp) cc_final: 0.8007 (tpp) REVERT: L 75 LYS cc_start: 0.9297 (mtmm) cc_final: 0.9092 (mtmm) outliers start: 19 outliers final: 16 residues processed: 71 average time/residue: 0.0888 time to fit residues: 10.1525 Evaluate side-chains 70 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 139 optimal weight: 0.0370 chunk 64 optimal weight: 0.0030 chunk 45 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.7472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.031085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.026753 restraints weight = 137222.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.027518 restraints weight = 68530.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028038 restraints weight = 43934.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.028382 restraints weight = 32569.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.028632 restraints weight = 26360.086| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12784 Z= 0.122 Angle : 0.499 8.014 17369 Z= 0.258 Chirality : 0.041 0.152 1896 Planarity : 0.004 0.040 2214 Dihedral : 4.129 29.073 1797 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.49 % Allowed : 10.48 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1579 helix: 1.17 (0.42), residues: 172 sheet: 0.19 (0.22), residues: 559 loop : -0.39 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 36 TYR 0.011 0.001 TYR I 49 PHE 0.007 0.001 PHE L 50 TRP 0.009 0.001 TRP J 47 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00284 (12765) covalent geometry : angle 0.49876 (17331) SS BOND : bond 0.00325 ( 19) SS BOND : angle 0.73567 ( 38) hydrogen bonds : bond 0.03001 ( 292) hydrogen bonds : angle 5.00773 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8405 (mmm) cc_final: 0.7951 (mmm) REVERT: A 202 MET cc_start: 0.9358 (ttm) cc_final: 0.9009 (ttp) REVERT: B 152 MET cc_start: 0.9143 (mmm) cc_final: 0.8907 (mmm) REVERT: E 18 MET cc_start: 0.8066 (mtp) cc_final: 0.7631 (tpp) REVERT: K 50 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.8100 (t80) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.0847 time to fit residues: 9.8291 Evaluate side-chains 69 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 33 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.030707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.026341 restraints weight = 140021.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027090 restraints weight = 70645.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.027607 restraints weight = 45746.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.027947 restraints weight = 34060.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028190 restraints weight = 27739.726| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12784 Z= 0.185 Angle : 0.548 8.630 17369 Z= 0.284 Chirality : 0.042 0.150 1896 Planarity : 0.004 0.041 2214 Dihedral : 4.322 29.696 1797 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.19 % Allowed : 11.22 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1579 helix: 1.08 (0.42), residues: 173 sheet: 0.15 (0.22), residues: 559 loop : -0.45 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.013 0.001 TYR I 49 PHE 0.010 0.001 PHE I 36 TRP 0.009 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00425 (12765) covalent geometry : angle 0.54720 (17331) SS BOND : bond 0.00396 ( 19) SS BOND : angle 0.87525 ( 38) hydrogen bonds : bond 0.03295 ( 292) hydrogen bonds : angle 5.16879 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8430 (mmm) cc_final: 0.7996 (mmm) REVERT: A 202 MET cc_start: 0.9346 (ttm) cc_final: 0.9007 (ttp) REVERT: B 152 MET cc_start: 0.9158 (mmm) cc_final: 0.8933 (mmm) REVERT: C 158 MET cc_start: 0.9239 (tpp) cc_final: 0.8609 (tpp) REVERT: K 4 MET cc_start: 0.8368 (ttt) cc_final: 0.7675 (ppp) REVERT: K 50 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (t80) outliers start: 16 outliers final: 15 residues processed: 65 average time/residue: 0.0836 time to fit residues: 8.7921 Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 100 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.031031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.026703 restraints weight = 137505.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027461 restraints weight = 68804.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.027979 restraints weight = 44193.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.028333 restraints weight = 32804.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.028572 restraints weight = 26479.969| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12784 Z= 0.109 Angle : 0.498 7.911 17369 Z= 0.256 Chirality : 0.041 0.155 1896 Planarity : 0.004 0.039 2214 Dihedral : 4.116 29.286 1797 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.34 % Allowed : 11.29 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.21), residues: 1579 helix: 1.29 (0.42), residues: 170 sheet: 0.19 (0.22), residues: 559 loop : -0.43 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 36 TYR 0.009 0.001 TYR I 49 PHE 0.006 0.001 PHE J 50 TRP 0.010 0.001 TRP J 47 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00256 (12765) covalent geometry : angle 0.49785 (17331) SS BOND : bond 0.00348 ( 19) SS BOND : angle 0.72877 ( 38) hydrogen bonds : bond 0.02893 ( 292) hydrogen bonds : angle 4.95839 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3158 Ramachandran restraints generated. 1579 Oldfield, 0 Emsley, 1579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8401 (mmm) cc_final: 0.7954 (mmm) REVERT: A 202 MET cc_start: 0.9348 (ttm) cc_final: 0.9025 (ttp) REVERT: B 152 MET cc_start: 0.9140 (mmm) cc_final: 0.8917 (mmm) REVERT: C 158 MET cc_start: 0.9166 (tpp) cc_final: 0.8647 (tpp) REVERT: H 34 MET cc_start: 0.9238 (mmm) cc_final: 0.8927 (tpp) REVERT: K 4 MET cc_start: 0.8271 (ttt) cc_final: 0.7789 (ppp) REVERT: K 50 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8068 (t80) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.1001 time to fit residues: 10.9346 Evaluate side-chains 69 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 0.0020 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.030634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.026292 restraints weight = 140361.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.027045 restraints weight = 70493.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.027558 restraints weight = 45565.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.027899 restraints weight = 33906.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.028133 restraints weight = 27583.202| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12784 Z= 0.179 Angle : 0.553 9.278 17369 Z= 0.285 Chirality : 0.042 0.150 1896 Planarity : 0.004 0.052 2214 Dihedral : 4.357 30.090 1797 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.34 % Allowed : 11.74 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.21), residues: 1579 helix: 1.20 (0.42), residues: 169 sheet: 0.14 (0.22), residues: 558 loop : -0.47 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 16 TYR 0.016 0.001 TYR F 79 PHE 0.009 0.001 PHE L 50 TRP 0.011 0.001 TRP G 91 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00411 (12765) covalent geometry : angle 0.55179 (17331) SS BOND : bond 0.00381 ( 19) SS BOND : angle 0.86075 ( 38) hydrogen bonds : bond 0.03338 ( 292) hydrogen bonds : angle 5.13234 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.55 seconds wall clock time: 30 minutes 3.23 seconds (1803.23 seconds total)