Starting phenix.real_space_refine on Wed Jun 11 02:41:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mr7_48554/06_2025/9mr7_48554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mr7_48554/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mr7_48554/06_2025/9mr7_48554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mr7_48554/06_2025/9mr7_48554.map" model { file = "/net/cci-nas-00/data/ceres_data/9mr7_48554/06_2025/9mr7_48554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mr7_48554/06_2025/9mr7_48554.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.04, per 1000 atoms: 0.65 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: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.50 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: 3.23 Time building geometry restraints manager: 3.55 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (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 TRP 0.013 0.001 TRP L 47 HIS 0.002 0.001 HIS E 47 PHE 0.017 0.002 PHE K 87 TYR 0.018 0.002 TYR L 33 ARG 0.027 0.002 ARG L 16 Details of bonding type rmsd hydrogen bonds : bond 0.26409 ( 292) hydrogen bonds : angle 8.18976 ( 777) SS BOND : bond 0.00476 ( 19) SS BOND : angle 1.34572 ( 38) covalent geometry : bond 0.00304 (12765) covalent geometry : angle 0.66704 (17331) *********************** 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 : 1.430 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: 0.3440 time to fit residues: 69.7889 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 : 1.420 ------------------------------------------------------------------------------- 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 131 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 141 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 12 GLN K 38 GLN K 79 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.031699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027256 restraints weight = 135121.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.028020 restraints weight = 67746.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.028543 restraints weight = 43890.978| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12784 Z= 0.211 Angle : 0.628 7.725 17369 Z= 0.330 Chirality : 0.044 0.205 1896 Planarity : 0.005 0.044 2214 Dihedral : 4.563 28.730 1797 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.04 % Allowed : 6.69 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1579 helix: 0.99 (0.42), residues: 164 sheet: -0.18 (0.22), residues: 556 loop : -0.79 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 35 HIS 0.004 0.001 HIS C 166 PHE 0.011 0.001 PHE I 36 TYR 0.020 0.002 TYR L 33 ARG 0.009 0.001 ARG L 38 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 292) hydrogen bonds : angle 6.31622 ( 777) SS BOND : bond 0.00517 ( 19) SS BOND : angle 1.05792 ( 38) covalent geometry : bond 0.00482 (12765) covalent geometry : angle 0.62633 (17331) *********************** 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 82 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.9010 (tp) cc_final: 0.8766 (tp) REVERT: C 16 GLN cc_start: 0.8748 (pm20) cc_final: 0.8517 (pm20) REVERT: C 170 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 11 MET cc_start: 0.8713 (mmm) cc_final: 0.8428 (mmm) REVERT: J 82 MET cc_start: 0.8955 (mtp) cc_final: 0.8612 (mtp) REVERT: K 103 LYS cc_start: 0.9118 (tppt) cc_final: 0.8869 (tptp) REVERT: L 18 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8790 (tt) REVERT: L 77 ILE cc_start: 0.9329 (mt) cc_final: 0.9069 (mm) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.2744 time to fit residues: 32.3659 Evaluate side-chains 67 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 155 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 HIS G 37 GLN I 89 GLN K 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.030188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025793 restraints weight = 142280.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026526 restraints weight = 72025.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027028 restraints weight = 47007.258| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 12784 Z= 0.295 Angle : 0.693 7.999 17369 Z= 0.363 Chirality : 0.045 0.185 1896 Planarity : 0.005 0.049 2214 Dihedral : 5.166 29.055 1797 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.26 % Allowed : 9.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1579 helix: 0.48 (0.41), residues: 166 sheet: -0.30 (0.22), residues: 560 loop : -0.77 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 96 HIS 0.006 0.002 HIS B 101 PHE 0.022 0.002 PHE I 36 TYR 0.024 0.002 TYR J 98 ARG 0.005 0.001 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 292) hydrogen bonds : angle 5.98852 ( 777) SS BOND : bond 0.00549 ( 19) SS BOND : angle 1.13247 ( 38) covalent geometry : bond 0.00667 (12765) covalent geometry : angle 0.69166 (17331) *********************** 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 75 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8312 (mmm) cc_final: 0.7964 (mmm) REVERT: A 202 MET cc_start: 0.9355 (ttm) cc_final: 0.8936 (ttp) REVERT: D 18 MET cc_start: 0.8314 (ttt) cc_final: 0.8026 (mtp) REVERT: H 34 MET cc_start: 0.9159 (tpp) cc_final: 0.8932 (mmm) REVERT: L 77 ILE cc_start: 0.9260 (mt) cc_final: 0.9048 (mm) outliers start: 17 outliers final: 10 residues processed: 72 average time/residue: 0.2491 time to fit residues: 27.6273 Evaluate side-chains 64 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 224 VAL 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 L residue 48 LEU Chi-restraints excluded: chain L residue 51 ILE 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 130 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.030769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026407 restraints weight = 137582.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027158 restraints weight = 69185.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.027674 restraints weight = 44779.998| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3181 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= 0.128 Angle : 0.531 7.604 17369 Z= 0.277 Chirality : 0.042 0.148 1896 Planarity : 0.004 0.044 2214 Dihedral : 4.572 28.876 1797 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.49 % Allowed : 10.55 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1579 helix: 0.99 (0.42), residues: 165 sheet: -0.20 (0.22), residues: 544 loop : -0.68 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 47 HIS 0.004 0.001 HIS B 101 PHE 0.008 0.001 PHE G 98 TYR 0.011 0.001 TYR I 49 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 292) hydrogen bonds : angle 5.37103 ( 777) SS BOND : bond 0.00408 ( 19) SS BOND : angle 0.81001 ( 38) covalent geometry : bond 0.00295 (12765) covalent geometry : angle 0.53058 (17331) *********************** 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 : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8327 (mmm) cc_final: 0.7935 (mmm) REVERT: A 202 MET cc_start: 0.9377 (ttm) cc_final: 0.9004 (ttp) REVERT: B 34 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 152 MET cc_start: 0.9112 (mmm) cc_final: 0.8858 (mmm) REVERT: C 158 MET cc_start: 0.9110 (tpp) cc_final: 0.8531 (tpp) outliers start: 20 outliers final: 12 residues processed: 77 average time/residue: 0.2535 time to fit residues: 31.1735 Evaluate side-chains 68 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 VAL Chi-restraints excluded: chain H residue 11 VAL 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 51 ILE Chi-restraints excluded: chain L residue 56 THR 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 151 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 139 optimal weight: 0.0570 chunk 115 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 = 0.3123 r_free = 0.3123 target = 0.031107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.026797 restraints weight = 136626.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.027530 restraints weight = 67675.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.028056 restraints weight = 44068.516| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12784 Z= 0.090 Angle : 0.498 8.619 17369 Z= 0.255 Chirality : 0.041 0.140 1896 Planarity : 0.004 0.040 2214 Dihedral : 4.186 28.910 1797 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1579 helix: 1.10 (0.41), residues: 171 sheet: -0.04 (0.22), residues: 541 loop : -0.56 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 52 HIS 0.002 0.000 HIS D 47 PHE 0.008 0.001 PHE J 50 TYR 0.013 0.001 TYR L 79 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 292) hydrogen bonds : angle 5.03217 ( 777) SS BOND : bond 0.00311 ( 19) SS BOND : angle 0.66101 ( 38) covalent geometry : bond 0.00208 (12765) covalent geometry : angle 0.49724 (17331) *********************** 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 76 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8369 (mmm) cc_final: 0.7925 (mmm) REVERT: A 202 MET cc_start: 0.9344 (ttm) cc_final: 0.8974 (ttp) REVERT: B 34 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 152 MET cc_start: 0.9123 (mmm) cc_final: 0.8896 (mmm) REVERT: C 158 MET cc_start: 0.9003 (tpp) cc_final: 0.8452 (tpp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.2282 time to fit residues: 26.0837 Evaluate side-chains 68 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 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 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 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.030561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026231 restraints weight = 141046.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.026974 restraints weight = 70226.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.027485 restraints weight = 45454.899| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3435 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= 0.165 Angle : 0.533 10.129 17369 Z= 0.276 Chirality : 0.041 0.138 1896 Planarity : 0.004 0.042 2214 Dihedral : 4.323 29.272 1797 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.49 % Allowed : 11.44 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1579 helix: 1.08 (0.41), residues: 172 sheet: 0.04 (0.22), residues: 550 loop : -0.54 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 PHE 0.010 0.001 PHE L 50 TYR 0.015 0.001 TYR L 79 ARG 0.006 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 292) hydrogen bonds : angle 5.13277 ( 777) SS BOND : bond 0.00396 ( 19) SS BOND : angle 0.80645 ( 38) covalent geometry : bond 0.00382 (12765) covalent geometry : angle 0.53246 (17331) *********************** 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: 20 poor density : 55 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8372 (mmm) cc_final: 0.7949 (mmm) REVERT: A 202 MET cc_start: 0.9342 (ttm) cc_final: 0.8933 (ttp) REVERT: B 34 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 152 MET cc_start: 0.9155 (mmm) cc_final: 0.8931 (mmm) REVERT: E 18 MET cc_start: 0.8466 (mtp) cc_final: 0.7700 (tpp) REVERT: E 28 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8619 (ptt) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.2174 time to fit residues: 24.3443 Evaluate side-chains 71 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 224 VAL 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 16 VAL Chi-restraints excluded: chain E residue 28 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 151 optimal weight: 0.0010 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.030694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026398 restraints weight = 138733.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.027144 restraints weight = 69032.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.027656 restraints weight = 44379.976| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3561 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= 0.129 Angle : 0.506 7.078 17369 Z= 0.262 Chirality : 0.041 0.162 1896 Planarity : 0.004 0.039 2214 Dihedral : 4.231 29.107 1797 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.86 % Allowed : 11.74 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1579 helix: 1.30 (0.42), residues: 166 sheet: 0.07 (0.22), residues: 549 loop : -0.50 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE I 36 TYR 0.013 0.001 TYR L 79 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 292) hydrogen bonds : angle 5.02149 ( 777) SS BOND : bond 0.00366 ( 19) SS BOND : angle 0.75957 ( 38) covalent geometry : bond 0.00299 (12765) covalent geometry : angle 0.50527 (17331) *********************** 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 84 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8374 (mmm) cc_final: 0.7951 (mmm) REVERT: A 202 MET cc_start: 0.9353 (ttm) cc_final: 0.8952 (ttp) REVERT: B 34 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7803 (tm-30) REVERT: B 35 LEU cc_start: 0.8941 (tp) cc_final: 0.8596 (tp) REVERT: B 152 MET cc_start: 0.9136 (mmm) cc_final: 0.8927 (mmm) REVERT: C 158 MET cc_start: 0.9135 (tpp) cc_final: 0.8603 (tpp) REVERT: E 18 MET cc_start: 0.8538 (mtp) cc_final: 0.7863 (tpp) REVERT: E 28 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (ptt) outliers start: 25 outliers final: 18 residues processed: 81 average time/residue: 0.2550 time to fit residues: 32.0692 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 : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 49 THR 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 D residue 95 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 28 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 H residue 96 LEU 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 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.031053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.026762 restraints weight = 137647.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027525 restraints weight = 68196.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028042 restraints weight = 43760.663| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3607 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= 0.091 Angle : 0.495 7.950 17369 Z= 0.253 Chirality : 0.041 0.136 1896 Planarity : 0.004 0.038 2214 Dihedral : 4.041 28.897 1797 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.71 % Allowed : 12.33 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1579 helix: 1.21 (0.42), residues: 172 sheet: 0.15 (0.22), residues: 549 loop : -0.48 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 52 HIS 0.002 0.000 HIS B 101 PHE 0.008 0.001 PHE J 50 TYR 0.010 0.001 TYR F 79 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.02791 ( 292) hydrogen bonds : angle 4.84399 ( 777) SS BOND : bond 0.00330 ( 19) SS BOND : angle 0.67828 ( 38) covalent geometry : bond 0.00216 (12765) covalent geometry : angle 0.49408 (17331) *********************** 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 80 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8347 (mmm) cc_final: 0.7921 (mmm) REVERT: A 202 MET cc_start: 0.9324 (ttm) cc_final: 0.8945 (ttp) REVERT: B 34 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 35 LEU cc_start: 0.8869 (tp) cc_final: 0.8528 (tp) REVERT: B 152 MET cc_start: 0.9121 (mmm) cc_final: 0.8915 (mmm) REVERT: C 158 MET cc_start: 0.9077 (tpp) cc_final: 0.8459 (tpp) REVERT: E 18 MET cc_start: 0.8494 (mtp) cc_final: 0.7891 (tpp) REVERT: H 34 MET cc_start: 0.9252 (mmm) cc_final: 0.8988 (tpp) outliers start: 23 outliers final: 16 residues processed: 77 average time/residue: 0.2598 time to fit residues: 31.7639 Evaluate side-chains 72 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 49 THR 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 16 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain L residue 48 LEU 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 120 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.030806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.026518 restraints weight = 139047.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.027276 restraints weight = 69372.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.027789 restraints weight = 44536.005| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3697 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= 0.129 Angle : 0.521 8.764 17369 Z= 0.265 Chirality : 0.041 0.133 1896 Planarity : 0.004 0.039 2214 Dihedral : 4.084 28.983 1797 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 12.18 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1579 helix: 1.31 (0.42), residues: 170 sheet: 0.16 (0.22), residues: 549 loop : -0.49 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE L 50 TYR 0.010 0.001 TYR I 49 ARG 0.004 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 292) hydrogen bonds : angle 4.90527 ( 777) SS BOND : bond 0.00360 ( 19) SS BOND : angle 0.72519 ( 38) covalent geometry : bond 0.00302 (12765) covalent geometry : angle 0.52033 (17331) *********************** 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 76 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8379 (mmm) cc_final: 0.7963 (mmm) REVERT: A 202 MET cc_start: 0.9351 (ttm) cc_final: 0.8974 (ttp) REVERT: B 34 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 152 MET cc_start: 0.9141 (mmm) cc_final: 0.8938 (mmm) REVERT: C 158 MET cc_start: 0.9118 (tpp) cc_final: 0.8468 (tpp) REVERT: E 64 MET cc_start: 0.9133 (mmp) cc_final: 0.8877 (mmp) outliers start: 22 outliers final: 20 residues processed: 73 average time/residue: 0.2999 time to fit residues: 34.8889 Evaluate side-chains 74 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 49 THR 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 D residue 95 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 96 LEU 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 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 134 optimal weight: 0.0670 chunk 20 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 0.0050 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9934 ------------------------------------------------------------------------------- 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 = 0.3124 r_free = 0.3124 target = 0.031142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.026858 restraints weight = 137200.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.027626 restraints weight = 68331.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.028143 restraints weight = 43803.789| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3739 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= 0.092 Angle : 0.501 8.933 17369 Z= 0.253 Chirality : 0.041 0.134 1896 Planarity : 0.004 0.037 2214 Dihedral : 3.942 28.711 1797 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 12.41 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1579 helix: 1.29 (0.41), residues: 170 sheet: 0.23 (0.23), residues: 542 loop : -0.45 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 52 HIS 0.002 0.000 HIS D 47 PHE 0.008 0.001 PHE J 50 TYR 0.007 0.001 TYR I 49 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.02748 ( 292) hydrogen bonds : angle 4.76921 ( 777) SS BOND : bond 0.00323 ( 19) SS BOND : angle 0.64919 ( 38) covalent geometry : bond 0.00219 (12765) covalent geometry : angle 0.50032 (17331) ********************** 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 76 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8355 (mmm) cc_final: 0.7920 (mmm) REVERT: A 202 MET cc_start: 0.9350 (ttm) cc_final: 0.8977 (ttp) REVERT: B 152 MET cc_start: 0.9127 (mmm) cc_final: 0.8917 (mmm) REVERT: C 158 MET cc_start: 0.9077 (tpp) cc_final: 0.8478 (tpp) REVERT: H 34 MET cc_start: 0.9219 (mmm) cc_final: 0.8957 (tpp) outliers start: 19 outliers final: 17 residues processed: 74 average time/residue: 0.2377 time to fit residues: 27.6400 Evaluate side-chains 71 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 49 THR 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 G residue 23 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 96 LEU 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 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 96 optimal weight: 0.0170 chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.4026 ------------------------------------------------------------------------------- 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 = 0.030683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026399 restraints weight = 139932.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.027129 restraints weight = 70072.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.027643 restraints weight = 45778.892| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12784 Z= 0.154 Angle : 0.539 8.631 17369 Z= 0.275 Chirality : 0.041 0.133 1896 Planarity : 0.004 0.038 2214 Dihedral : 4.123 29.071 1797 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.49 % Allowed : 12.41 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1579 helix: 1.21 (0.41), residues: 170 sheet: 0.15 (0.23), residues: 548 loop : -0.46 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 91 HIS 0.003 0.001 HIS B 101 PHE 0.008 0.001 PHE I 36 TYR 0.018 0.001 TYR F 79 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 292) hydrogen bonds : angle 4.92723 ( 777) SS BOND : bond 0.00363 ( 19) SS BOND : angle 0.77499 ( 38) covalent geometry : bond 0.00358 (12765) covalent geometry : angle 0.53846 (17331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.06 seconds wall clock time: 63 minutes 48.68 seconds (3828.68 seconds total)