Starting phenix.real_space_refine on Wed May 14 22:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mr7_48554/05_2025/9mr7_48554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mr7_48554/05_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_48554/05_2025/9mr7_48554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mr7_48554/05_2025/9mr7_48554.map" model { file = "/net/cci-nas-00/data/ceres_data/9mr7_48554/05_2025/9mr7_48554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mr7_48554/05_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-5687/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: 7.48, per 1000 atoms: 0.60 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: 2.46 Conformation dependent library (CDL) restraints added in 1.5 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: 1.36 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: 3.27 Time building geometry restraints manager: 2.99 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: 6.060 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.240 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- 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 : 1.353 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: 0.3330 time to fit residues: 67.9263 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 : 1.341 ------------------------------------------------------------------------------- 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 = 135121.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.028020 restraints weight = 67741.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.028541 restraints weight = 43881.639| |-----------------------------------------------------------------------------| 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 6.31624 ( 777) SS BOND : bond 0.00517 ( 19) SS BOND : angle 1.05794 ( 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 : 1.465 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: 0.8749 (pm20) cc_final: 0.8517 (pm20) REVERT: C 170 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 11 MET cc_start: 0.8712 (mmm) cc_final: 0.8425 (mmm) REVERT: J 82 MET cc_start: 0.8953 (mtp) cc_final: 0.8612 (mtp) REVERT: K 103 LYS cc_start: 0.9119 (tppt) cc_final: 0.8869 (tptp) REVERT: L 18 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8788 (tt) REVERT: L 77 ILE cc_start: 0.9328 (mt) cc_final: 0.9069 (mm) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.2477 time to fit residues: 29.1112 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 : 1.292 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 chunk 130 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 47 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 = 0.3122 r_free = 0.3122 target = 0.031260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.026873 restraints weight = 138049.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.027616 restraints weight = 68796.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.028138 restraints weight = 44724.236| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12784 Z= 0.168 Angle : 0.557 5.911 17369 Z= 0.291 Chirality : 0.042 0.176 1896 Planarity : 0.004 0.045 2214 Dihedral : 4.494 28.481 1797 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.97 % Allowed : 9.58 % Favored : 89.45 % 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: -0.47 (0.21), residues: 1579 helix: 1.03 (0.42), residues: 165 sheet: -0.08 (0.22), residues: 547 loop : -0.68 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.004 0.001 HIS B 101 PHE 0.011 0.001 PHE I 36 TYR 0.014 0.001 TYR I 49 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 292) hydrogen bonds : angle 5.70709 ( 777) SS BOND : bond 0.00454 ( 19) SS BOND : angle 0.90009 ( 38) covalent geometry : bond 0.00381 (12765) covalent geometry : angle 0.55624 (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 74 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8461 (mmm) cc_final: 0.7870 (mmm) REVERT: C 158 MET cc_start: 0.9100 (tpp) cc_final: 0.8445 (tpp) REVERT: D 11 MET cc_start: 0.8821 (mmm) cc_final: 0.8564 (mmm) REVERT: D 18 MET cc_start: 0.8209 (ttt) cc_final: 0.7933 (mtp) REVERT: E 18 MET cc_start: 0.8385 (mtp) cc_final: 0.8114 (mtp) REVERT: J 82 MET cc_start: 0.8978 (mtp) cc_final: 0.8497 (mtp) outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.2244 time to fit residues: 24.5643 Evaluate side-chains 66 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 130 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 94 optimal weight: 4.9990 overall best weight: 0.8378 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.031726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.027375 restraints weight = 135076.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028151 restraints weight = 66959.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.028675 restraints weight = 42946.993| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2727 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= 0.090 Angle : 0.498 7.685 17369 Z= 0.257 Chirality : 0.042 0.150 1896 Planarity : 0.004 0.039 2214 Dihedral : 4.113 28.149 1797 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.26 % Allowed : 9.88 % Favored : 88.86 % 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: -0.25 (0.21), residues: 1579 helix: 1.22 (0.42), residues: 165 sheet: 0.09 (0.22), residues: 547 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 B 101 PHE 0.006 0.001 PHE D 52 TYR 0.010 0.001 TYR L 79 ARG 0.003 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 292) hydrogen bonds : angle 5.16672 ( 777) SS BOND : bond 0.00373 ( 19) SS BOND : angle 0.63809 ( 38) covalent geometry : bond 0.00204 (12765) covalent geometry : angle 0.49813 (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 78 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.8451 (mmm) cc_final: 0.7808 (mmm) REVERT: C 158 MET cc_start: 0.8900 (tpp) cc_final: 0.8439 (tpp) REVERT: D 11 MET cc_start: 0.8816 (mmm) cc_final: 0.8568 (mmm) REVERT: D 57 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8624 (mmtm) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 0.2425 time to fit residues: 27.2302 Evaluate side-chains 66 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 E residue 80 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 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: 5.9990 chunk 24 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.030986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.026635 restraints weight = 138910.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027388 restraints weight = 69473.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.027902 restraints weight = 44881.407| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3039 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= 0.183 Angle : 0.549 8.462 17369 Z= 0.284 Chirality : 0.042 0.144 1896 Planarity : 0.004 0.043 2214 Dihedral : 4.334 28.534 1797 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.41 % Allowed : 10.85 % Favored : 87.74 % 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: -0.30 (0.21), residues: 1579 helix: 1.07 (0.42), residues: 172 sheet: 0.01 (0.22), residues: 555 loop : -0.54 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 47 HIS 0.003 0.001 HIS B 101 PHE 0.011 0.001 PHE I 36 TYR 0.016 0.001 TYR J 98 ARG 0.005 0.000 ARG C 36 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 292) hydrogen bonds : angle 5.23845 ( 777) SS BOND : bond 0.00395 ( 19) SS BOND : angle 0.91283 ( 38) covalent geometry : bond 0.00420 (12765) covalent geometry : angle 0.54795 (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 74 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.389 Fit side-chains REVERT: A 194 MET cc_start: 0.8447 (mmm) cc_final: 0.7787 (mmm) REVERT: B 152 MET cc_start: 0.9128 (mmm) cc_final: 0.8888 (mmm) REVERT: D 11 MET cc_start: 0.8827 (mmm) cc_final: 0.8609 (mmm) REVERT: E 18 MET cc_start: 0.8419 (mtp) cc_final: 0.8163 (mtp) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.2274 time to fit residues: 25.3354 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 : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL 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 H residue 11 VAL Chi-restraints excluded: chain H residue 87 THR 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9209 > 50: distance: 33 - 185: 6.431 distance: 68 - 171: 11.736 distance: 71 - 168: 5.424 distance: 85 - 152: 13.043 distance: 88 - 149: 22.272 distance: 112 - 131: 21.193 distance: 124 - 131: 20.795 distance: 131 - 132: 12.628 distance: 132 - 133: 35.349 distance: 132 - 135: 25.029 distance: 133 - 134: 17.432 distance: 133 - 139: 30.457 distance: 135 - 136: 26.589 distance: 136 - 137: 19.073 distance: 136 - 138: 20.396 distance: 139 - 140: 17.675 distance: 140 - 141: 22.118 distance: 140 - 143: 23.232 distance: 141 - 142: 25.232 distance: 141 - 144: 37.133 distance: 144 - 145: 24.789 distance: 145 - 146: 21.464 distance: 145 - 148: 30.939 distance: 146 - 147: 25.706 distance: 146 - 149: 6.041 distance: 149 - 150: 7.741 distance: 150 - 151: 24.007 distance: 150 - 153: 26.543 distance: 151 - 152: 6.073 distance: 151 - 156: 17.563 distance: 153 - 154: 17.726 distance: 153 - 155: 14.982 distance: 156 - 157: 17.688 distance: 156 - 275: 16.986 distance: 157 - 158: 14.803 distance: 157 - 160: 7.517 distance: 158 - 159: 11.673 distance: 158 - 168: 15.682 distance: 159 - 272: 10.404 distance: 160 - 161: 22.322 distance: 161 - 162: 19.959 distance: 161 - 163: 19.389 distance: 162 - 164: 6.869 distance: 163 - 165: 15.816 distance: 164 - 166: 6.088 distance: 165 - 166: 7.831 distance: 166 - 167: 14.941 distance: 168 - 169: 8.770 distance: 169 - 170: 6.153 distance: 170 - 171: 8.397 distance: 170 - 180: 7.363 distance: 172 - 173: 7.723 distance: 173 - 174: 4.495 distance: 173 - 175: 4.820 distance: 174 - 176: 10.504 distance: 175 - 177: 8.154 distance: 176 - 178: 4.526 distance: 178 - 179: 11.721 distance: 181 - 182: 6.722 distance: 181 - 184: 6.139 distance: 182 - 183: 15.064 distance: 182 - 186: 4.909 distance: 184 - 185: 11.082 distance: 186 - 187: 6.486 distance: 187 - 188: 8.916 distance: 187 - 190: 6.795 distance: 188 - 189: 17.131 distance: 188 - 195: 14.397 distance: 190 - 191: 10.914 distance: 191 - 192: 7.578 distance: 192 - 193: 8.480 distance: 192 - 194: 10.173 distance: 195 - 196: 8.031 distance: 195 - 246: 3.459 distance: 196 - 197: 7.715 distance: 196 - 199: 11.904 distance: 197 - 198: 28.182 distance: 197 - 204: 5.968 distance: 199 - 200: 12.457 distance: 201 - 202: 11.296 distance: 201 - 203: 5.574 distance: 204 - 205: 4.966 distance: 205 - 206: 5.318 distance: 205 - 208: 23.493 distance: 206 - 207: 9.300 distance: 206 - 218: 11.101 distance: 208 - 209: 8.052 distance: 209 - 210: 9.674 distance: 209 - 211: 12.274 distance: 210 - 212: 12.530 distance: 211 - 213: 4.270 distance: 211 - 214: 13.560 distance: 212 - 213: 13.679 distance: 213 - 215: 11.864 distance: 214 - 216: 8.287 distance: 215 - 217: 8.767 distance: 216 - 217: 9.243