Starting phenix.real_space_refine on Mon Mar 18 12:14:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/03_2024/8hla_34859_updated.pdb" } resolution = 2.81 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= 0.001 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 60 5.16 5 C 13596 2.51 5 N 3372 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I GLU 204": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 174": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 121": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "L ARG 133": "NH1" <-> "NH2" Residue "L GLU 148": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20868 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "D" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "G" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "I" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "K" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1726 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'FL3': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'FL3': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.51, per 1000 atoms: 0.50 Number of scatterers: 20868 At special positions: 0 Unit cell: (163.777, 160.485, 71.601, 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 60 16.00 O 3840 8.00 N 3372 7.00 C 13596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.03 Conformation dependent library (CDL) restraints added in 3.5 seconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 25 sheets defined 33.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.038A pdb=" N ALA A 27 " --> pdb=" O PRO A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.361A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'B' and resid 25 through 28 No H-bonds generated for 'chain 'B' and resid 25 through 28' Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 75 through 89 removed outlier: 5.960A pdb=" N LYS B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 188 through 200 removed outlier: 4.417A pdb=" N ALA B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 27 removed outlier: 4.338A pdb=" N PHE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 146 through 162 Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'D' and resid 22 through 25 No H-bonds generated for 'chain 'D' and resid 22 through 25' Processing helix chain 'D' and resid 43 through 55 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 146 through 162 removed outlier: 3.707A pdb=" N ASP D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 199 removed outlier: 3.584A pdb=" N GLU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 25 No H-bonds generated for 'chain 'E' and resid 22 through 25' Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 57 through 61 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 101 through 109 removed outlier: 3.634A pdb=" N GLU E 104 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 105 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 106 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 109 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 162 Processing helix chain 'E' and resid 188 through 200 Processing helix chain 'F' and resid 22 through 28 removed outlier: 3.795A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 27 " --> pdb=" O PRO F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 57 through 61 Processing helix chain 'F' and resid 75 through 88 Processing helix chain 'F' and resid 105 through 108 No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 146 through 162 Processing helix chain 'F' and resid 193 through 200 removed outlier: 3.756A pdb=" N LYS F 198 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 3.947A pdb=" N PHE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 27 " --> pdb=" O PRO G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 55 Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 75 through 88 removed outlier: 3.733A pdb=" N GLU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 109 Processing helix chain 'G' and resid 146 through 161 removed outlier: 3.515A pdb=" N ASP G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 22 through 25 No H-bonds generated for 'chain 'H' and resid 22 through 25' Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 57 through 62 Processing helix chain 'H' and resid 75 through 88 Processing helix chain 'H' and resid 101 through 108 removed outlier: 3.834A pdb=" N GLU H 104 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU H 105 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 162 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 22 through 25 No H-bonds generated for 'chain 'I' and resid 22 through 25' Processing helix chain 'I' and resid 44 through 61 removed outlier: 4.832A pdb=" N ASP I 58 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 removed outlier: 6.182A pdb=" N LYS I 80 " --> pdb=" O CYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 109 removed outlier: 3.653A pdb=" N GLU I 104 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU I 105 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 25 through 28 No H-bonds generated for 'chain 'J' and resid 25 through 28' Processing helix chain 'J' and resid 44 through 55 Processing helix chain 'J' and resid 57 through 63 removed outlier: 3.619A pdb=" N LEU J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 88 removed outlier: 5.937A pdb=" N LYS J 80 " --> pdb=" O CYS J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 108 removed outlier: 3.635A pdb=" N GLU J 104 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU J 105 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA J 106 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 161 Processing helix chain 'J' and resid 188 through 200 removed outlier: 3.540A pdb=" N ALA J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 25 No H-bonds generated for 'chain 'K' and resid 22 through 25' Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 57 through 62 Processing helix chain 'K' and resid 75 through 88 Processing helix chain 'K' and resid 101 through 108 removed outlier: 4.420A pdb=" N GLU K 104 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU K 105 " --> pdb=" O ARG K 102 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA K 106 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP K 107 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 162 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'L' and resid 22 through 25 No H-bonds generated for 'chain 'L' and resid 22 through 25' Processing helix chain 'L' and resid 45 through 55 Processing helix chain 'L' and resid 57 through 62 Processing helix chain 'L' and resid 75 through 88 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 146 through 161 Processing helix chain 'L' and resid 189 through 191 No H-bonds generated for 'chain 'L' and resid 189 through 191' Processing helix chain 'L' and resid 193 through 196 No H-bonds generated for 'chain 'L' and resid 193 through 196' Processing sheet with id= A, first strand: chain 'A' and resid 65 through 70 removed outlier: 6.528A pdb=" N TRP A 32 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 68 " --> pdb=" O TRP A 32 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 34 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 70 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 36 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA A 122 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 134 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 12 through 15 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 138 removed outlier: 3.681A pdb=" N ILE B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 125 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 135 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 123 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 137 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG B 121 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER B 71 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 98 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 12 through 15 Processing sheet with id= E, first strand: chain 'C' and resid 65 through 70 removed outlier: 6.762A pdb=" N TRP C 32 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE C 68 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 34 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 70 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE C 36 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 122 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 134 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 132 through 138 removed outlier: 6.314A pdb=" N ILE D 125 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 135 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 123 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 137 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG D 121 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER D 71 " --> pdb=" O PRO D 96 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE D 98 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 12 through 15 removed outlier: 3.567A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 132 through 138 removed outlier: 6.288A pdb=" N ILE E 125 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 135 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL E 123 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR E 137 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG E 121 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N SER E 71 " --> pdb=" O PRO E 96 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE E 98 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 12 through 15 Processing sheet with id= J, first strand: chain 'F' and resid 132 through 138 removed outlier: 6.503A pdb=" N ILE F 125 " --> pdb=" O ARG F 133 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 135 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 123 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR F 137 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG F 121 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER F 71 " --> pdb=" O PRO F 96 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE F 98 " --> pdb=" O SER F 71 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 203 through 205 Processing sheet with id= L, first strand: chain 'G' and resid 12 through 15 Processing sheet with id= M, first strand: chain 'G' and resid 132 through 138 removed outlier: 6.421A pdb=" N ILE G 125 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE G 135 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 123 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR G 137 " --> pdb=" O ARG G 121 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG G 121 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SER G 71 " --> pdb=" O PRO G 96 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 98 " --> pdb=" O SER G 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 12 through 15 Processing sheet with id= O, first strand: chain 'H' and resid 132 through 138 removed outlier: 6.383A pdb=" N ILE H 125 " --> pdb=" O ARG H 133 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 135 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 123 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR H 137 " --> pdb=" O ARG H 121 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG H 121 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER H 71 " --> pdb=" O PRO H 96 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE H 98 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 12 through 15 removed outlier: 3.984A pdb=" N GLY I 18 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 97 through 99 removed outlier: 6.565A pdb=" N GLY I 69 " --> pdb=" O ILE I 98 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA I 134 " --> pdb=" O ILE I 125 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 12 through 15 Processing sheet with id= S, first strand: chain 'J' and resid 132 through 138 removed outlier: 6.584A pdb=" N ILE J 125 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE J 135 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL J 123 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR J 137 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG J 121 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N SER J 71 " --> pdb=" O PRO J 96 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE J 98 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 203 through 205 removed outlier: 3.736A pdb=" N GLU J 204 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 12 through 15 Processing sheet with id= V, first strand: chain 'K' and resid 65 through 68 removed outlier: 6.489A pdb=" N TRP K 32 " --> pdb=" O GLU K 66 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE K 68 " --> pdb=" O TRP K 32 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL K 34 " --> pdb=" O ILE K 68 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 69 through 71 Processing sheet with id= X, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.980A pdb=" N GLY L 18 " --> pdb=" O THR L 15 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 132 through 139 removed outlier: 6.387A pdb=" N ILE L 125 " --> pdb=" O ARG L 133 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE L 135 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL L 123 " --> pdb=" O ILE L 135 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR L 137 " --> pdb=" O ARG L 121 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG L 121 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N SER L 71 " --> pdb=" O PRO L 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE L 98 " --> pdb=" O SER L 71 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1911 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: 8.15 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6337 1.33 - 1.45: 3584 1.45 - 1.57: 11391 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 21420 Sorted by residual: bond pdb=" C TYR I 137 " pdb=" N TYR I 138 " ideal model delta sigma weight residual 1.331 1.287 0.044 1.48e-02 4.57e+03 8.79e+00 bond pdb=" C TYR A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 1.329 1.277 0.052 1.86e-02 2.89e+03 7.87e+00 bond pdb=" CA ARG B 121 " pdb=" CB ARG B 121 " ideal model delta sigma weight residual 1.536 1.433 0.103 4.10e-02 5.95e+02 6.29e+00 bond pdb=" CG1 ILE A 79 " pdb=" CD1 ILE A 79 " ideal model delta sigma weight residual 1.513 1.417 0.096 3.90e-02 6.57e+02 6.12e+00 bond pdb=" C TYR K 137 " pdb=" N TYR K 138 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.47e-02 4.63e+03 6.00e+00 ... (remaining 21415 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.81: 349 103.81 - 111.42: 8960 111.42 - 119.03: 8583 119.03 - 126.64: 10690 126.64 - 134.25: 482 Bond angle restraints: 29064 Sorted by residual: angle pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" N GLY A 201 " pdb=" CA GLY A 201 " pdb=" C GLY A 201 " ideal model delta sigma weight residual 114.95 108.29 6.66 1.41e+00 5.03e-01 2.23e+01 angle pdb=" N LYS F 192 " pdb=" CA LYS F 192 " pdb=" C LYS F 192 " ideal model delta sigma weight residual 113.18 107.28 5.90 1.33e+00 5.65e-01 1.97e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 112.29 108.17 4.12 9.40e-01 1.13e+00 1.92e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 110.80 120.09 -9.29 2.13e+00 2.20e-01 1.90e+01 ... (remaining 29059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 11374 17.52 - 35.04: 1050 35.04 - 52.56: 198 52.56 - 70.08: 30 70.08 - 87.60: 20 Dihedral angle restraints: 12672 sinusoidal: 5208 harmonic: 7464 Sorted by residual: dihedral pdb=" CA GLN A 193 " pdb=" C GLN A 193 " pdb=" N ARG A 194 " pdb=" CA ARG A 194 " ideal model delta harmonic sigma weight residual -180.00 -129.59 -50.41 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA GLY A 103 " pdb=" C GLY A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta harmonic sigma weight residual -180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 12669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2486 0.078 - 0.155: 606 0.155 - 0.233: 37 0.233 - 0.311: 13 0.311 - 0.388: 2 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB ILE A 68 " pdb=" CA ILE A 68 " pdb=" CG1 ILE A 68 " pdb=" CG2 ILE A 68 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB VAL E 164 " pdb=" CA VAL E 164 " pdb=" CG1 VAL E 164 " pdb=" CG2 VAL E 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 3141 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 26 " -0.054 2.00e-02 2.50e+03 5.27e-02 4.86e+01 pdb=" CG PHE J 26 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE J 26 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE J 26 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE J 26 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE J 26 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE J 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 43 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO L 44 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 32 " 0.028 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP G 32 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP G 32 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 32 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 32 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 32 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 352 2.60 - 3.18: 19592 3.18 - 3.75: 35957 3.75 - 4.33: 53110 4.33 - 4.90: 84235 Nonbonded interactions: 193246 Sorted by model distance: nonbonded pdb=" OH TYR A 138 " pdb=" OE2 GLU B 148 " model vdw 2.027 2.440 nonbonded pdb=" OG1 THR I 187 " pdb=" OD1 ASP I 189 " model vdw 2.033 2.440 nonbonded pdb=" O PRO H 183 " pdb=" NH2 ARG H 194 " model vdw 2.044 2.520 nonbonded pdb=" OE2 GLU C 148 " pdb=" OH TYR D 138 " model vdw 2.083 2.440 nonbonded pdb=" OE2 GLU G 148 " pdb=" OH TYR H 138 " model vdw 2.111 2.440 ... (remaining 193241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'B' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'C' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'D' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'E' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'F' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'G' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'H' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'I' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'J' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'K' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) selection = (chain 'L' and (resid 1 through 41 or resid 43 through 75 or resid 77 through 21 \ 5)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.420 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 56.190 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:15.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.011 0.106 21420 Z= 0.696 Angle : 0.955 12.780 29064 Z= 0.513 Chirality : 0.065 0.388 3144 Planarity : 0.006 0.105 3684 Dihedral : 14.251 87.604 7848 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 0.09 % Allowed : 1.22 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2556 helix: -1.34 (0.16), residues: 858 sheet: -1.64 (0.27), residues: 353 loop : -1.61 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP G 32 HIS 0.021 0.003 HIS D 78 PHE 0.119 0.004 PHE J 26 TYR 0.027 0.003 TYR A 212 ARG 0.007 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 412 time to evaluate : 1.823 Fit side-chains REVERT: B 45 VAL cc_start: 0.7569 (p) cc_final: 0.7320 (t) REVERT: B 86 LYS cc_start: 0.7995 (tttm) cc_final: 0.7767 (tttp) REVERT: D 108 LYS cc_start: 0.7431 (mptt) cc_final: 0.6900 (mmtp) REVERT: E 88 ASN cc_start: 0.8710 (m110) cc_final: 0.8487 (m-40) REVERT: I 100 ASP cc_start: 0.8129 (t70) cc_final: 0.7762 (OUTLIER) REVERT: I 200 LYS cc_start: 0.7260 (ptpt) cc_final: 0.6879 (ptpt) REVERT: K 148 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6629 (tp30) outliers start: 2 outliers final: 2 residues processed: 413 average time/residue: 1.2516 time to fit residues: 588.0531 Evaluate side-chains 301 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 136 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 191 optimal weight: 0.0020 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN H 193 GLN I 17 HIS K 29 GLN L 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21420 Z= 0.213 Angle : 0.668 14.819 29064 Z= 0.339 Chirality : 0.049 0.176 3144 Planarity : 0.005 0.090 3684 Dihedral : 6.063 47.209 2749 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.56 % Rotamer: Outliers : 2.03 % Allowed : 12.07 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.16), residues: 2556 helix: -0.12 (0.17), residues: 872 sheet: -1.52 (0.28), residues: 337 loop : -1.39 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 32 HIS 0.006 0.001 HIS B 168 PHE 0.019 0.002 PHE F 8 TYR 0.022 0.002 TYR L 212 ARG 0.006 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 356 time to evaluate : 2.315 Fit side-chains REVERT: A 63 LEU cc_start: 0.7937 (tt) cc_final: 0.7684 (mp) REVERT: B 45 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7114 (t) REVERT: B 53 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6756 (tpp) REVERT: C 7 LYS cc_start: 0.7197 (tppt) cc_final: 0.6654 (tptt) REVERT: D 4 ILE cc_start: 0.8095 (mm) cc_final: 0.7806 (mm) REVERT: E 88 ASN cc_start: 0.8632 (m110) cc_final: 0.8424 (m-40) REVERT: F 53 MET cc_start: 0.8127 (tpp) cc_final: 0.7817 (tpp) REVERT: G 49 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7488 (mt-10) REVERT: G 188 VAL cc_start: 0.7791 (t) cc_final: 0.7562 (m) REVERT: H 82 MET cc_start: 0.7785 (mtp) cc_final: 0.7550 (mtp) REVERT: I 100 ASP cc_start: 0.8106 (t70) cc_final: 0.7847 (t70) REVERT: I 178 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8017 (p0) REVERT: I 200 LYS cc_start: 0.7237 (ptpt) cc_final: 0.6817 (ptpt) REVERT: J 1 MET cc_start: 0.5934 (tpp) cc_final: 0.5509 (tpt) REVERT: L 1 MET cc_start: 0.5026 (tpt) cc_final: 0.4763 (tpp) outliers start: 45 outliers final: 14 residues processed: 379 average time/residue: 1.1846 time to fit residues: 514.8428 Evaluate side-chains 334 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 317 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain I residue 92 GLU Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 173 ASN D 193 GLN G 193 GLN H 193 GLN I 193 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21420 Z= 0.276 Angle : 0.651 13.712 29064 Z= 0.329 Chirality : 0.049 0.164 3144 Planarity : 0.005 0.087 3684 Dihedral : 5.857 47.537 2749 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 3.06 % Allowed : 15.68 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2556 helix: 0.22 (0.17), residues: 872 sheet: -1.48 (0.28), residues: 331 loop : -1.33 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 208 HIS 0.006 0.001 HIS D 78 PHE 0.019 0.002 PHE I 33 TYR 0.023 0.002 TYR L 212 ARG 0.005 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 324 time to evaluate : 2.428 Fit side-chains revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 107 ASP cc_start: 0.7447 (m-30) cc_final: 0.7240 (m-30) REVERT: B 45 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7124 (t) REVERT: B 56 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7394 (ptm160) REVERT: B 73 ASP cc_start: 0.7115 (m-30) cc_final: 0.6913 (m-30) REVERT: C 7 LYS cc_start: 0.7175 (tppt) cc_final: 0.6633 (tptt) REVERT: C 24 ASP cc_start: 0.7239 (p0) cc_final: 0.6910 (m-30) REVERT: C 49 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8152 (mt-10) REVERT: E 14 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7407 (mtpt) REVERT: E 88 ASN cc_start: 0.8653 (m110) cc_final: 0.8436 (m-40) REVERT: G 49 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7609 (mt-10) REVERT: G 188 VAL cc_start: 0.7858 (t) cc_final: 0.7643 (m) REVERT: H 82 MET cc_start: 0.7779 (mtp) cc_final: 0.7544 (mtp) REVERT: H 193 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7391 (pt0) REVERT: I 24 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: I 200 LYS cc_start: 0.7263 (ptpt) cc_final: 0.6743 (ptpt) REVERT: J 104 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6957 (mt-10) REVERT: K 7 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6805 (tttm) REVERT: L 1 MET cc_start: 0.5243 (tpt) cc_final: 0.5006 (tpp) outliers start: 68 outliers final: 33 residues processed: 365 average time/residue: 1.1336 time to fit residues: 477.7256 Evaluate side-chains 346 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 306 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain E residue 14 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 78 HIS Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 193 GLN Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain J residue 26 PHE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 181 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9758 > 50: distance: 10 - 15: 31.190 distance: 15 - 16: 20.267 distance: 16 - 17: 24.620 distance: 16 - 19: 22.390 distance: 17 - 18: 23.749 distance: 17 - 20: 27.927 distance: 20 - 21: 4.728 distance: 21 - 22: 13.936 distance: 21 - 24: 12.191 distance: 22 - 23: 5.734 distance: 22 - 28: 12.673 distance: 24 - 25: 14.584 distance: 25 - 26: 7.845 distance: 25 - 27: 10.484 distance: 28 - 29: 27.994 distance: 29 - 30: 31.290 distance: 29 - 32: 9.541 distance: 30 - 31: 41.045 distance: 30 - 39: 9.676 distance: 32 - 33: 16.889 distance: 33 - 34: 13.090 distance: 33 - 35: 10.125 distance: 34 - 36: 16.294 distance: 35 - 37: 17.869 distance: 36 - 38: 19.862 distance: 37 - 38: 18.026 distance: 39 - 40: 5.541 distance: 40 - 41: 38.532 distance: 40 - 43: 17.307 distance: 41 - 42: 28.258 distance: 41 - 46: 10.210 distance: 43 - 44: 48.272 distance: 43 - 45: 39.321 distance: 46 - 47: 10.741 distance: 46 - 52: 6.354 distance: 47 - 48: 8.737 distance: 47 - 50: 14.919 distance: 48 - 49: 20.462 distance: 48 - 53: 11.209 distance: 49 - 73: 36.801 distance: 50 - 51: 15.130 distance: 51 - 52: 30.971 distance: 53 - 54: 9.263 distance: 54 - 57: 6.810 distance: 55 - 56: 17.945 distance: 55 - 60: 13.626 distance: 56 - 80: 12.495 distance: 57 - 58: 15.325 distance: 57 - 59: 17.929 distance: 60 - 61: 10.507 distance: 61 - 62: 6.140 distance: 61 - 64: 14.023 distance: 62 - 63: 10.144 distance: 62 - 66: 17.328 distance: 63 - 89: 12.401 distance: 64 - 65: 27.352 distance: 66 - 67: 24.088 distance: 67 - 68: 28.121 distance: 67 - 70: 11.123 distance: 68 - 69: 11.377 distance: 68 - 73: 7.435 distance: 69 - 97: 12.302 distance: 70 - 71: 23.830 distance: 70 - 72: 31.327 distance: 73 - 74: 25.611 distance: 74 - 77: 14.443 distance: 75 - 76: 18.862 distance: 75 - 80: 17.480 distance: 76 - 104: 22.849 distance: 77 - 78: 21.408 distance: 77 - 79: 13.965 distance: 80 - 81: 17.988 distance: 81 - 82: 9.861 distance: 81 - 84: 17.539 distance: 82 - 83: 13.150 distance: 82 - 89: 7.875 distance: 83 - 109: 19.086 distance: 84 - 85: 14.692 distance: 85 - 86: 7.141 distance: 86 - 87: 10.299 distance: 86 - 88: 3.901