Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 20:15:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/04_2023/8hla_34859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/04_2023/8hla_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_34859/04_2023/8hla_34859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/04_2023/8hla_34859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/04_2023/8hla_34859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hla_34859/04_2023/8hla_34859_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 11.36, per 1000 atoms: 0.54 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: 8.86 Conformation dependent library (CDL) restraints added in 3.1 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: 1.53 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: 5.83 Time building geometry restraints manager: 9.46 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.640 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 53.230 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.080 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.390 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.438 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 413 average time/residue: 1.2575 time to fit residues: 593.8501 Evaluate side-chains 299 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2644 time to fit residues: 4.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 K 54 GLN L 74 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21420 Z= 0.208 Angle : 0.663 14.784 29064 Z= 0.336 Chirality : 0.049 0.185 3144 Planarity : 0.005 0.087 3684 Dihedral : 5.977 46.954 2748 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.76 % Rotamer Outliers : 1.98 % 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: -1.45 (0.16), residues: 2556 helix: -0.09 (0.17), residues: 872 sheet: -1.53 (0.28), residues: 337 loop : -1.37 (0.16), residues: 1347 *********************** 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 404 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 360 time to evaluate : 2.413 Fit side-chains outliers start: 44 outliers final: 15 residues processed: 381 average time/residue: 1.2013 time to fit residues: 525.8497 Evaluate side-chains 333 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 318 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.4275 time to fit residues: 7.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN D 193 GLN G 193 GLN H 193 GLN I 193 GLN K 54 GLN L 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 21420 Z= 0.262 Angle : 0.645 13.547 29064 Z= 0.326 Chirality : 0.049 0.164 3144 Planarity : 0.005 0.086 3684 Dihedral : 5.735 47.572 2748 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer Outliers : 2.84 % 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: -1.20 (0.16), residues: 2556 helix: 0.26 (0.17), residues: 872 sheet: -1.49 (0.28), residues: 336 loop : -1.31 (0.16), residues: 1348 *********************** 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 388 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 325 time to evaluate : 2.525 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 33 residues processed: 365 average time/residue: 1.1748 time to fit residues: 494.9779 Evaluate side-chains 331 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 298 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 21 residues processed: 13 average time/residue: 0.4670 time to fit residues: 11.4988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 193 GLN I 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 21420 Z= 0.261 Angle : 0.632 12.734 29064 Z= 0.320 Chirality : 0.049 0.169 3144 Planarity : 0.005 0.086 3684 Dihedral : 5.611 50.036 2748 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer Outliers : 3.11 % 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: -1.08 (0.16), residues: 2556 helix: 0.42 (0.17), residues: 878 sheet: -1.47 (0.28), residues: 331 loop : -1.27 (0.16), residues: 1347 *********************** REFINEMENT MACRO_CYCLE 4 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 388 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 319 time to evaluate : 2.439 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 42 residues processed: 369 average time/residue: 1.1405 time to fit residues: 487.9413 Evaluate side-chains 332 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 290 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 31 residues processed: 12 average time/residue: 0.5616 time to fit residues: 11.9593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 21420 Z= 0.290 Angle : 0.645 12.488 29064 Z= 0.325 Chirality : 0.049 0.206 3144 Planarity : 0.005 0.087 3684 Dihedral : 5.628 51.135 2748 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Rotamer Outliers : 3.47 % 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: -1.04 (0.16), residues: 2556 helix: 0.46 (0.17), residues: 878 sheet: -1.47 (0.28), residues: 331 loop : -1.25 (0.16), residues: 1347 *********************** REFINEMENT MACRO_CYCLE 5 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 395 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 318 time to evaluate : 2.564 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 49 residues processed: 370 average time/residue: 1.1066 time to fit residues: 477.2993 Evaluate side-chains 345 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 296 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 35 residues processed: 15 average time/residue: 0.2294 time to fit residues: 9.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN G 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.109 21420 Z= 0.478 Angle : 0.733 13.807 29064 Z= 0.373 Chirality : 0.053 0.187 3144 Planarity : 0.005 0.095 3684 Dihedral : 5.984 52.394 2748 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer Outliers : 3.42 % 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: -1.35 (0.16), residues: 2556 helix: 0.06 (0.17), residues: 878 sheet: -1.52 (0.27), residues: 346 loop : -1.35 (0.16), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 6 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 385 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 309 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 56 residues processed: 365 average time/residue: 1.1363 time to fit residues: 482.4326 Evaluate side-chains 350 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 294 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 43 residues processed: 14 average time/residue: 0.2134 time to fit residues: 8.7171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 0.2980 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN I 193 GLN L 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21420 Z= 0.193 Angle : 0.616 12.555 29064 Z= 0.309 Chirality : 0.048 0.192 3144 Planarity : 0.004 0.089 3684 Dihedral : 5.472 50.825 2748 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer Outliers : 3.29 % 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: -0.93 (0.16), residues: 2556 helix: 0.61 (0.18), residues: 874 sheet: -1.45 (0.27), residues: 336 loop : -1.21 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 7 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: 73 poor density : 328 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 50 residues processed: 378 average time/residue: 1.1448 time to fit residues: 502.8710 Evaluate side-chains 346 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 2.464 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 39 residues processed: 11 average time/residue: 0.3704 time to fit residues: 9.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 193 GLN L 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21420 Z= 0.220 Angle : 0.628 13.318 29064 Z= 0.315 Chirality : 0.048 0.236 3144 Planarity : 0.004 0.089 3684 Dihedral : 5.402 51.214 2748 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer Outliers : 2.75 % 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: -0.82 (0.16), residues: 2556 helix: 0.71 (0.18), residues: 874 sheet: -1.36 (0.27), residues: 336 loop : -1.16 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 8 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 375 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 314 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 46 residues processed: 365 average time/residue: 1.0827 time to fit residues: 458.7514 Evaluate side-chains 333 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 287 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 5 average time/residue: 0.1966 time to fit residues: 4.0862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 21420 Z= 0.399 Angle : 0.701 12.333 29064 Z= 0.355 Chirality : 0.052 0.216 3144 Planarity : 0.005 0.094 3684 Dihedral : 5.757 53.475 2748 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.30 % Favored : 93.58 % Rotamer Outliers : 2.70 % 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: -1.10 (0.16), residues: 2556 helix: 0.31 (0.17), residues: 874 sheet: -1.37 (0.28), residues: 336 loop : -1.23 (0.16), residues: 1346 *********************** REFINEMENT MACRO_CYCLE 9 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 369 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 309 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 44 residues processed: 362 average time/residue: 1.0892 time to fit residues: 460.0619 Evaluate side-chains 340 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 296 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 42 residues processed: 3 average time/residue: 0.2830 time to fit residues: 4.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN I 193 GLN L 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 21420 Z= 0.322 Angle : 0.681 13.079 29064 Z= 0.343 Chirality : 0.050 0.208 3144 Planarity : 0.005 0.093 3684 Dihedral : 5.708 53.428 2748 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.94 % Rotamer Outliers : 2.30 % 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: -1.10 (0.16), residues: 2556 helix: 0.34 (0.17), residues: 874 sheet: -1.39 (0.27), residues: 336 loop : -1.25 (0.16), residues: 1346 ********************** REFINEMENT MACRO_CYCLE 10 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 357 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 45 residues processed: 354 average time/residue: 1.1069 time to fit residues: 458.2963 Evaluate side-chains 343 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 43 residues processed: 2 average time/residue: 0.2855 time to fit residues: 4.3973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN L 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.168310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.137357 restraints weight = 24020.195| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.08 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21420 Z= 0.211 Angle : 0.637 13.803 29064 Z= 0.317 Chirality : 0.048 0.265 3144 Planarity : 0.004 0.089 3684 Dihedral : 5.441 52.059 2748 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer Outliers : 2.39 % 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: -0.83 (0.16), residues: 2556 helix: 0.68 (0.18), residues: 869 sheet: -1.29 (0.28), residues: 336 loop : -1.17 (0.16), residues: 1351 =============================================================================== Job complete usr+sys time: 7950.74 seconds wall clock time: 143 minutes 25.94 seconds (8605.94 seconds total)