Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 20:50:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k22_22640/10_2023/7k22_22640.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 1.000 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 120 5.16 5 C 13745 2.51 5 N 3610 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L1 ARG 24": "NH1" <-> "NH2" Residue "L1 ARG 61": "NH1" <-> "NH2" Residue "L1 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 GLU 81": "OE1" <-> "OE2" Residue "L1 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 ASP 42": "OD1" <-> "OD2" Residue "H1 GLU 61": "OE1" <-> "OE2" Residue "H1 ARG 62": "NH1" <-> "NH2" Residue "H1 ARG 67": "NH1" <-> "NH2" Residue "H1 ARG 77": "NH1" <-> "NH2" Residue "H1 ASP 85": "OD1" <-> "OD2" Residue "H1 ARG 95": "NH1" <-> "NH2" Residue "H1 ASP 103": "OD1" <-> "OD2" Residue "F1 GLU 35": "OE1" <-> "OE2" Residue "F1 ASP 38": "OD1" <-> "OD2" Residue "F1 ASP 44": "OD1" <-> "OD2" Residue "F1 GLU 50": "OE1" <-> "OE2" Residue "F1 GLU 64": "OE1" <-> "OE2" Residue "F1 GLU 68": "OE1" <-> "OE2" Residue "F1 ASP 85": "OD1" <-> "OD2" Residue "F1 GLU 91": "OE1" <-> "OE2" Residue "F1 ASP 111": "OD1" <-> "OD2" Residue "F1 GLU 121": "OE1" <-> "OE2" Residue "F1 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 ASP 173": "OD1" <-> "OD2" Residue "F1 ASP 219": "OD1" <-> "OD2" Residue "F1 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 344": "OE1" <-> "OE2" Residue "F1 ASP 355": "OD1" <-> "OD2" Residue "L2 ARG 24": "NH1" <-> "NH2" Residue "L2 ARG 61": "NH1" <-> "NH2" Residue "L2 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 GLU 81": "OE1" <-> "OE2" Residue "L2 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 ASP 42": "OD1" <-> "OD2" Residue "H2 GLU 61": "OE1" <-> "OE2" Residue "H2 ARG 62": "NH1" <-> "NH2" Residue "H2 ARG 67": "NH1" <-> "NH2" Residue "H2 ARG 77": "NH1" <-> "NH2" Residue "H2 ASP 85": "OD1" <-> "OD2" Residue "H2 ARG 95": "NH1" <-> "NH2" Residue "H2 ASP 103": "OD1" <-> "OD2" Residue "F2 GLU 35": "OE1" <-> "OE2" Residue "F2 ASP 38": "OD1" <-> "OD2" Residue "F2 ASP 44": "OD1" <-> "OD2" Residue "F2 GLU 50": "OE1" <-> "OE2" Residue "F2 GLU 64": "OE1" <-> "OE2" Residue "F2 GLU 68": "OE1" <-> "OE2" Residue "F2 ASP 85": "OD1" <-> "OD2" Residue "F2 GLU 91": "OE1" <-> "OE2" Residue "F2 ASP 111": "OD1" <-> "OD2" Residue "F2 GLU 121": "OE1" <-> "OE2" Residue "F2 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 ASP 173": "OD1" <-> "OD2" Residue "F2 ASP 219": "OD1" <-> "OD2" Residue "F2 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 344": "OE1" <-> "OE2" Residue "F2 ASP 355": "OD1" <-> "OD2" Residue "L3 ARG 24": "NH1" <-> "NH2" Residue "L3 ARG 61": "NH1" <-> "NH2" Residue "L3 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L3 GLU 81": "OE1" <-> "OE2" Residue "L3 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H3 ASP 42": "OD1" <-> "OD2" Residue "H3 GLU 61": "OE1" <-> "OE2" Residue "H3 ARG 62": "NH1" <-> "NH2" Residue "H3 ARG 67": "NH1" <-> "NH2" Residue "H3 ARG 77": "NH1" <-> "NH2" Residue "H3 ASP 85": "OD1" <-> "OD2" Residue "H3 ARG 95": "NH1" <-> "NH2" Residue "H3 ASP 103": "OD1" <-> "OD2" Residue "F3 GLU 35": "OE1" <-> "OE2" Residue "F3 ASP 38": "OD1" <-> "OD2" Residue "F3 ASP 44": "OD1" <-> "OD2" Residue "F3 GLU 50": "OE1" <-> "OE2" Residue "F3 GLU 64": "OE1" <-> "OE2" Residue "F3 GLU 68": "OE1" <-> "OE2" Residue "F3 ASP 85": "OD1" <-> "OD2" Residue "F3 GLU 91": "OE1" <-> "OE2" Residue "F3 ASP 111": "OD1" <-> "OD2" Residue "F3 GLU 121": "OE1" <-> "OE2" Residue "F3 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 ASP 173": "OD1" <-> "OD2" Residue "F3 ASP 219": "OD1" <-> "OD2" Residue "F3 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 344": "OE1" <-> "OE2" Residue "F3 ASP 355": "OD1" <-> "OD2" Residue "L4 ARG 24": "NH1" <-> "NH2" Residue "L4 ARG 61": "NH1" <-> "NH2" Residue "L4 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L4 GLU 81": "OE1" <-> "OE2" Residue "L4 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H4 ASP 42": "OD1" <-> "OD2" Residue "H4 GLU 61": "OE1" <-> "OE2" Residue "H4 ARG 62": "NH1" <-> "NH2" Residue "H4 ARG 67": "NH1" <-> "NH2" Residue "H4 ARG 77": "NH1" <-> "NH2" Residue "H4 ASP 85": "OD1" <-> "OD2" Residue "H4 ARG 95": "NH1" <-> "NH2" Residue "H4 ASP 103": "OD1" <-> "OD2" Residue "F4 GLU 35": "OE1" <-> "OE2" Residue "F4 ASP 38": "OD1" <-> "OD2" Residue "F4 ASP 44": "OD1" <-> "OD2" Residue "F4 GLU 50": "OE1" <-> "OE2" Residue "F4 GLU 64": "OE1" <-> "OE2" Residue "F4 GLU 68": "OE1" <-> "OE2" Residue "F4 ASP 85": "OD1" <-> "OD2" Residue "F4 GLU 91": "OE1" <-> "OE2" Residue "F4 ASP 111": "OD1" <-> "OD2" Residue "F4 GLU 121": "OE1" <-> "OE2" Residue "F4 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 ASP 173": "OD1" <-> "OD2" Residue "F4 ASP 219": "OD1" <-> "OD2" Residue "F4 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 GLU 344": "OE1" <-> "OE2" Residue "F4 ASP 355": "OD1" <-> "OD2" Residue "L5 ARG 24": "NH1" <-> "NH2" Residue "L5 ARG 61": "NH1" <-> "NH2" Residue "L5 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 GLU 81": "OE1" <-> "OE2" Residue "L5 TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H5 ASP 42": "OD1" <-> "OD2" Residue "H5 GLU 61": "OE1" <-> "OE2" Residue "H5 ARG 62": "NH1" <-> "NH2" Residue "H5 ARG 67": "NH1" <-> "NH2" Residue "H5 ARG 77": "NH1" <-> "NH2" Residue "H5 ASP 85": "OD1" <-> "OD2" Residue "H5 ARG 95": "NH1" <-> "NH2" Residue "H5 ASP 103": "OD1" <-> "OD2" Residue "F5 GLU 35": "OE1" <-> "OE2" Residue "F5 ASP 38": "OD1" <-> "OD2" Residue "F5 ASP 44": "OD1" <-> "OD2" Residue "F5 GLU 50": "OE1" <-> "OE2" Residue "F5 GLU 64": "OE1" <-> "OE2" Residue "F5 GLU 68": "OE1" <-> "OE2" Residue "F5 ASP 85": "OD1" <-> "OD2" Residue "F5 GLU 91": "OE1" <-> "OE2" Residue "F5 ASP 111": "OD1" <-> "OD2" Residue "F5 GLU 121": "OE1" <-> "OE2" Residue "F5 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 ASP 173": "OD1" <-> "OD2" Residue "F5 ASP 219": "OD1" <-> "OD2" Residue "F5 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 344": "OE1" <-> "OE2" Residue "F5 ASP 355": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 21665 Number of models: 1 Model: "" Number of chains: 15 Chain: "L1" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H1" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F1" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "L2" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H2" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F2" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "L3" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H3" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F3" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "L4" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H4" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F4" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "L5" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 770 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Chain: "H5" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 813 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "F5" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Time building chain proxies: 10.91, per 1000 atoms: 0.50 Number of scatterers: 21665 At special positions: 0 Unit cell: (140.8, 136.4, 124.3, 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 120 16.00 O 4190 8.00 N 3610 7.00 C 13745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYSL1 23 " - pdb=" SG CYSL1 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH1 18 " - pdb=" SG CYSH1 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF1 19 " - pdb=" SG CYSF2 114 " distance=2.03 Simple disulfide: pdb=" SG CYSF1 114 " - pdb=" SG CYSF5 19 " distance=2.03 Simple disulfide: pdb=" SG CYSL2 23 " - pdb=" SG CYSL2 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 18 " - pdb=" SG CYSH2 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF2 19 " - pdb=" SG CYSF3 114 " distance=2.06 Simple disulfide: pdb=" SG CYSL3 23 " - pdb=" SG CYSL3 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH3 18 " - pdb=" SG CYSH3 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF3 19 " - pdb=" SG CYSF4 114 " distance=2.07 Simple disulfide: pdb=" SG CYSL4 23 " - pdb=" SG CYSL4 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH4 18 " - pdb=" SG CYSH4 91 " distance=2.03 Simple disulfide: pdb=" SG CYSF4 19 " - pdb=" SG CYSF5 114 " distance=1.93 Simple disulfide: pdb=" SG CYSL5 23 " - pdb=" SG CYSL5 88 " distance=2.03 Simple disulfide: pdb=" SG CYSH5 18 " - pdb=" SG CYSH5 91 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.4 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 45 sheets defined 11.1% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'L1' and resid 50 through 52 No H-bonds generated for 'chain 'L1' and resid 50 through 52' Processing helix chain 'L1' and resid 79 through 83 removed outlier: 3.630A pdb=" N LEUL1 83 " --> pdb=" O THRL1 80 " (cutoff:3.500A) Processing helix chain 'H1' and resid 24 through 28 removed outlier: 3.507A pdb=" N SERH1 27 " --> pdb=" O THRH1 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRH1 28 " --> pdb=" O PHEH1 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 24 through 28' Processing helix chain 'H1' and resid 57 through 60 removed outlier: 3.982A pdb=" N LYSH1 60 " --> pdb=" O ASPH1 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 57 through 60' Processing helix chain 'F1' and resid 33 through 39 Processing helix chain 'F1' and resid 91 through 95 Processing helix chain 'F1' and resid 132 through 137 Processing helix chain 'F1' and resid 192 through 197 removed outlier: 3.597A pdb=" N ILEF1 196 " --> pdb=" O THRF1 192 " (cutoff:3.500A) Processing helix chain 'F1' and resid 202 through 207 Processing helix chain 'F1' and resid 320 through 322 No H-bonds generated for 'chain 'F1' and resid 320 through 322' Processing helix chain 'F1' and resid 323 through 333 Processing helix chain 'L2' and resid 50 through 52 No H-bonds generated for 'chain 'L2' and resid 50 through 52' Processing helix chain 'L2' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL2 83 " --> pdb=" O THRL2 80 " (cutoff:3.500A) Processing helix chain 'H2' and resid 24 through 28 removed outlier: 3.505A pdb=" N SERH2 27 " --> pdb=" O THRH2 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH2 28 " --> pdb=" O PHEH2 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 24 through 28' Processing helix chain 'H2' and resid 57 through 60 removed outlier: 3.984A pdb=" N LYSH2 60 " --> pdb=" O ASPH2 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 57 through 60' Processing helix chain 'F2' and resid 33 through 39 Processing helix chain 'F2' and resid 91 through 95 Processing helix chain 'F2' and resid 132 through 137 Processing helix chain 'F2' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF2 196 " --> pdb=" O THRF2 192 " (cutoff:3.500A) Processing helix chain 'F2' and resid 202 through 207 Processing helix chain 'F2' and resid 320 through 322 No H-bonds generated for 'chain 'F2' and resid 320 through 322' Processing helix chain 'F2' and resid 323 through 333 Processing helix chain 'L3' and resid 50 through 52 No H-bonds generated for 'chain 'L3' and resid 50 through 52' Processing helix chain 'L3' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL3 83 " --> pdb=" O THRL3 80 " (cutoff:3.500A) Processing helix chain 'H3' and resid 24 through 28 removed outlier: 3.506A pdb=" N SERH3 27 " --> pdb=" O THRH3 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH3 28 " --> pdb=" O PHEH3 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 24 through 28' Processing helix chain 'H3' and resid 57 through 60 removed outlier: 3.983A pdb=" N LYSH3 60 " --> pdb=" O ASPH3 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H3' and resid 57 through 60' Processing helix chain 'F3' and resid 33 through 39 Processing helix chain 'F3' and resid 91 through 95 Processing helix chain 'F3' and resid 132 through 137 Processing helix chain 'F3' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF3 196 " --> pdb=" O THRF3 192 " (cutoff:3.500A) Processing helix chain 'F3' and resid 202 through 207 Processing helix chain 'F3' and resid 320 through 322 No H-bonds generated for 'chain 'F3' and resid 320 through 322' Processing helix chain 'F3' and resid 323 through 333 Processing helix chain 'L4' and resid 50 through 52 No H-bonds generated for 'chain 'L4' and resid 50 through 52' Processing helix chain 'L4' and resid 79 through 83 removed outlier: 3.630A pdb=" N LEUL4 83 " --> pdb=" O THRL4 80 " (cutoff:3.500A) Processing helix chain 'H4' and resid 24 through 28 removed outlier: 3.505A pdb=" N SERH4 27 " --> pdb=" O THRH4 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYRH4 28 " --> pdb=" O PHEH4 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 24 through 28' Processing helix chain 'H4' and resid 57 through 60 removed outlier: 3.983A pdb=" N LYSH4 60 " --> pdb=" O ASPH4 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H4' and resid 57 through 60' Processing helix chain 'F4' and resid 33 through 39 Processing helix chain 'F4' and resid 91 through 95 Processing helix chain 'F4' and resid 132 through 137 Processing helix chain 'F4' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF4 196 " --> pdb=" O THRF4 192 " (cutoff:3.500A) Processing helix chain 'F4' and resid 202 through 207 Processing helix chain 'F4' and resid 320 through 322 No H-bonds generated for 'chain 'F4' and resid 320 through 322' Processing helix chain 'F4' and resid 323 through 333 Processing helix chain 'L5' and resid 50 through 52 No H-bonds generated for 'chain 'L5' and resid 50 through 52' Processing helix chain 'L5' and resid 79 through 83 removed outlier: 3.629A pdb=" N LEUL5 83 " --> pdb=" O THRL5 80 " (cutoff:3.500A) Processing helix chain 'H5' and resid 24 through 28 removed outlier: 3.506A pdb=" N SERH5 27 " --> pdb=" O THRH5 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRH5 28 " --> pdb=" O PHEH5 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 24 through 28' Processing helix chain 'H5' and resid 57 through 60 removed outlier: 3.984A pdb=" N LYSH5 60 " --> pdb=" O ASPH5 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H5' and resid 57 through 60' Processing helix chain 'F5' and resid 33 through 39 Processing helix chain 'F5' and resid 91 through 95 Processing helix chain 'F5' and resid 132 through 137 Processing helix chain 'F5' and resid 192 through 197 removed outlier: 3.598A pdb=" N ILEF5 196 " --> pdb=" O THRF5 192 " (cutoff:3.500A) Processing helix chain 'F5' and resid 202 through 207 Processing helix chain 'F5' and resid 320 through 322 No H-bonds generated for 'chain 'F5' and resid 320 through 322' Processing helix chain 'F5' and resid 323 through 333 Processing sheet with id=AA1, first strand: chain 'L1' and resid 4 through 6 removed outlier: 6.155A pdb=" N THRL1 69 " --> pdb=" O ALAL1 25 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N GLNL1 27 " --> pdb=" O SERL1 67 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N SERL1 67 " --> pdb=" O GLNL1 27 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N VALL1 29 " --> pdb=" O SERL1 65 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N SERL1 65 " --> pdb=" O VALL1 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L1' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL1 35 " --> pdb=" O VALL1 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL1 49 " --> pdb=" O VALL1 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL1 33 " --> pdb=" O TYRL1 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H1' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH1 73 " --> pdb=" O ASPH1 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H1' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH1 41 " --> pdb=" O VALH1 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH1 36 " --> pdb=" O LEUH1 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH1 43 " --> pdb=" O ARGH1 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH1 34 " --> pdb=" O TRPH1 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F1' and resid 46 through 53 removed outlier: 6.512A pdb=" N TYRF1 305 " --> pdb=" O THRF1 127 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THRF1 127 " --> pdb=" O TYRF1 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF1 307 " --> pdb=" O VALF1 125 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VALF1 125 " --> pdb=" O LYSF1 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF1 309 " --> pdb=" O VALF1 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F1' and resid 99 through 104 removed outlier: 6.535A pdb=" N ARGF1 300 " --> pdb=" O METF1 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF1 288 " --> pdb=" O HISF1 298 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HISF1 298 " --> pdb=" O TRPF1 288 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F1' and resid 99 through 104 Processing sheet with id=AA8, first strand: chain 'F1' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF1 153 " --> pdb=" O PROF1 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F1' and resid 213 through 215 Processing sheet with id=AB1, first strand: chain 'F1' and resid 252 through 256 Processing sheet with id=AB2, first strand: chain 'F1' and resid 252 through 256 removed outlier: 6.534A pdb=" N ARGF2 300 " --> pdb=" O METF2 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRPF2 288 " --> pdb=" O HISF2 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF2 298 " --> pdb=" O TRPF2 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L2' and resid 4 through 6 removed outlier: 6.155A pdb=" N THRL2 69 " --> pdb=" O ALAL2 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL2 27 " --> pdb=" O SERL2 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL2 67 " --> pdb=" O GLNL2 27 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N VALL2 29 " --> pdb=" O SERL2 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL2 65 " --> pdb=" O VALL2 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L2' and resid 53 through 54 removed outlier: 6.446A pdb=" N TRPL2 35 " --> pdb=" O VALL2 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL2 49 " --> pdb=" O VALL2 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL2 33 " --> pdb=" O TYRL2 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H2' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH2 73 " --> pdb=" O ASPH2 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H2' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH2 41 " --> pdb=" O VALH2 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH2 36 " --> pdb=" O LEUH2 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH2 43 " --> pdb=" O ARGH2 34 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARGH2 34 " --> pdb=" O TRPH2 43 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F2' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF2 305 " --> pdb=" O THRF2 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF2 127 " --> pdb=" O TYRF2 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF2 307 " --> pdb=" O VALF2 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF2 125 " --> pdb=" O LYSF2 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF2 309 " --> pdb=" O VALF2 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F2' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF2 153 " --> pdb=" O PROF2 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F2' and resid 213 through 215 Processing sheet with id=AC1, first strand: chain 'F2' and resid 252 through 256 Processing sheet with id=AC2, first strand: chain 'F2' and resid 252 through 256 removed outlier: 6.534A pdb=" N ARGF3 300 " --> pdb=" O METF3 286 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRPF3 288 " --> pdb=" O HISF3 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF3 298 " --> pdb=" O TRPF3 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L3' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL3 69 " --> pdb=" O ALAL3 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL3 27 " --> pdb=" O SERL3 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL3 67 " --> pdb=" O GLNL3 27 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N VALL3 29 " --> pdb=" O SERL3 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL3 65 " --> pdb=" O VALL3 29 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L3' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL3 35 " --> pdb=" O VALL3 47 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYRL3 49 " --> pdb=" O VALL3 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL3 33 " --> pdb=" O TYRL3 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H3' and resid 18 through 19 removed outlier: 3.803A pdb=" N THRH3 73 " --> pdb=" O ASPH3 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H3' and resid 53 through 55 removed outlier: 5.605A pdb=" N LEUH3 41 " --> pdb=" O VALH3 36 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VALH3 36 " --> pdb=" O LEUH3 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH3 43 " --> pdb=" O ARGH3 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH3 34 " --> pdb=" O TRPH3 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F3' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF3 305 " --> pdb=" O THRF3 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF3 127 " --> pdb=" O TYRF3 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF3 307 " --> pdb=" O VALF3 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF3 125 " --> pdb=" O LYSF3 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF3 309 " --> pdb=" O VALF3 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F3' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF3 153 " --> pdb=" O PROF3 144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F3' and resid 213 through 215 Processing sheet with id=AD1, first strand: chain 'F3' and resid 252 through 256 Processing sheet with id=AD2, first strand: chain 'F3' and resid 252 through 256 removed outlier: 6.535A pdb=" N ARGF4 300 " --> pdb=" O METF4 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF4 288 " --> pdb=" O HISF4 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF4 298 " --> pdb=" O TRPF4 288 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L4' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL4 69 " --> pdb=" O ALAL4 25 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N GLNL4 27 " --> pdb=" O SERL4 67 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SERL4 67 " --> pdb=" O GLNL4 27 " (cutoff:3.500A) removed outlier: 12.020A pdb=" N VALL4 29 " --> pdb=" O SERL4 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL4 65 " --> pdb=" O VALL4 29 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L4' and resid 53 through 54 removed outlier: 6.446A pdb=" N TRPL4 35 " --> pdb=" O VALL4 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYRL4 49 " --> pdb=" O VALL4 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VALL4 33 " --> pdb=" O TYRL4 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H4' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH4 73 " --> pdb=" O ASPH4 68 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H4' and resid 53 through 55 removed outlier: 5.605A pdb=" N LEUH4 41 " --> pdb=" O VALH4 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH4 36 " --> pdb=" O LEUH4 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRPH4 43 " --> pdb=" O ARGH4 34 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARGH4 34 " --> pdb=" O TRPH4 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F4' and resid 46 through 53 removed outlier: 6.512A pdb=" N TYRF4 305 " --> pdb=" O THRF4 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF4 127 " --> pdb=" O TYRF4 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF4 307 " --> pdb=" O VALF4 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF4 125 " --> pdb=" O LYSF4 307 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THRF4 309 " --> pdb=" O VALF4 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F4' and resid 144 through 146 removed outlier: 6.188A pdb=" N ILEF4 153 " --> pdb=" O PROF4 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F4' and resid 213 through 215 Processing sheet with id=AE1, first strand: chain 'F4' and resid 252 through 256 Processing sheet with id=AE2, first strand: chain 'F4' and resid 252 through 256 removed outlier: 6.535A pdb=" N ARGF5 300 " --> pdb=" O METF5 286 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRPF5 288 " --> pdb=" O HISF5 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HISF5 298 " --> pdb=" O TRPF5 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L5' and resid 4 through 6 removed outlier: 6.156A pdb=" N THRL5 69 " --> pdb=" O ALAL5 25 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N GLNL5 27 " --> pdb=" O SERL5 67 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N SERL5 67 " --> pdb=" O GLNL5 27 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N VALL5 29 " --> pdb=" O SERL5 65 " (cutoff:3.500A) removed outlier: 11.695A pdb=" N SERL5 65 " --> pdb=" O VALL5 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L5' and resid 53 through 54 removed outlier: 6.447A pdb=" N TRPL5 35 " --> pdb=" O VALL5 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TYRL5 49 " --> pdb=" O VALL5 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VALL5 33 " --> pdb=" O TYRL5 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H5' and resid 18 through 19 removed outlier: 3.802A pdb=" N THRH5 73 " --> pdb=" O ASPH5 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H5' and resid 53 through 55 removed outlier: 5.606A pdb=" N LEUH5 41 " --> pdb=" O VALH5 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALH5 36 " --> pdb=" O LEUH5 41 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRPH5 43 " --> pdb=" O ARGH5 34 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARGH5 34 " --> pdb=" O TRPH5 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F5' and resid 46 through 53 removed outlier: 6.513A pdb=" N TYRF5 305 " --> pdb=" O THRF5 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THRF5 127 " --> pdb=" O TYRF5 305 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSF5 307 " --> pdb=" O VALF5 125 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALF5 125 " --> pdb=" O LYSF5 307 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THRF5 309 " --> pdb=" O VALF5 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F5' and resid 144 through 146 removed outlier: 6.189A pdb=" N ILEF5 153 " --> pdb=" O PROF5 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F5' and resid 213 through 215 646 hydrogen bonds defined for protein. 1503 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: 6.76 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6960 1.34 - 1.46: 4681 1.46 - 1.57: 10384 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 22225 Sorted by residual: bond pdb=" CA GLNF2 71 " pdb=" C GLNF2 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.48e+00 bond pdb=" CA GLNF3 71 " pdb=" C GLNF3 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.44e+00 bond pdb=" CA GLNF1 71 " pdb=" C GLNF1 71 " ideal model delta sigma weight residual 1.532 1.517 0.015 9.60e-03 1.09e+04 2.42e+00 bond pdb=" CA GLNF5 71 " pdb=" C GLNF5 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.26e+00 bond pdb=" CA GLNF4 71 " pdb=" C GLNF4 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.13e+00 ... (remaining 22220 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.58: 891 106.58 - 113.48: 11926 113.48 - 120.37: 8111 120.37 - 127.27: 9055 127.27 - 134.16: 307 Bond angle restraints: 30290 Sorted by residual: angle pdb=" C ALAF3 18 " pdb=" N CYSF3 19 " pdb=" CA CYSF3 19 " ideal model delta sigma weight residual 121.48 111.28 10.20 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF5 18 " pdb=" N CYSF5 19 " pdb=" CA CYSF5 19 " ideal model delta sigma weight residual 121.48 111.28 10.20 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF2 18 " pdb=" N CYSF2 19 " pdb=" CA CYSF2 19 " ideal model delta sigma weight residual 121.48 111.29 10.19 2.04e+00 2.40e-01 2.50e+01 angle pdb=" C ALAF4 18 " pdb=" N CYSF4 19 " pdb=" CA CYSF4 19 " ideal model delta sigma weight residual 121.48 111.30 10.18 2.04e+00 2.40e-01 2.49e+01 angle pdb=" C ALAF1 18 " pdb=" N CYSF1 19 " pdb=" CA CYSF1 19 " ideal model delta sigma weight residual 121.48 111.32 10.16 2.04e+00 2.40e-01 2.48e+01 ... (remaining 30285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11379 17.30 - 34.60: 1367 34.60 - 51.89: 334 51.89 - 69.19: 135 69.19 - 86.49: 30 Dihedral angle restraints: 13245 sinusoidal: 5295 harmonic: 7950 Sorted by residual: dihedral pdb=" CB CYSF3 19 " pdb=" SG CYSF3 19 " pdb=" SG CYSF4 114 " pdb=" CB CYSF4 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.84 64.84 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYSF1 19 " pdb=" SG CYSF1 19 " pdb=" SG CYSF2 114 " pdb=" CB CYSF2 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.70 64.70 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYSF4 19 " pdb=" SG CYSF4 19 " pdb=" SG CYSF5 114 " pdb=" CB CYSF5 114 " ideal model delta sinusoidal sigma weight residual -86.00 -150.44 64.44 1 1.00e+01 1.00e-02 5.46e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1941 0.036 - 0.072: 1007 0.072 - 0.108: 282 0.108 - 0.144: 88 0.144 - 0.181: 17 Chirality restraints: 3335 Sorted by residual: chirality pdb=" CA THRF3 62 " pdb=" N THRF3 62 " pdb=" C THRF3 62 " pdb=" CB THRF3 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA THRF1 62 " pdb=" N THRF1 62 " pdb=" C THRF1 62 " pdb=" CB THRF1 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA THRF4 62 " pdb=" N THRF4 62 " pdb=" C THRF4 62 " pdb=" CB THRF4 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 3332 not shown) Planarity restraints: 3905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERF4 89 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PROF4 90 " 0.109 5.00e-02 4.00e+02 pdb=" CA PROF4 90 " -0.033 5.00e-02 4.00e+02 pdb=" CD PROF4 90 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF3 89 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PROF3 90 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROF3 90 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROF3 90 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF2 89 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PROF2 90 " -0.109 5.00e-02 4.00e+02 pdb=" CA PROF2 90 " 0.033 5.00e-02 4.00e+02 pdb=" CD PROF2 90 " 0.035 5.00e-02 4.00e+02 ... (remaining 3902 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 424 2.65 - 3.21: 19012 3.21 - 3.77: 31867 3.77 - 4.34: 46117 4.34 - 4.90: 76935 Nonbonded interactions: 174355 Sorted by model distance: nonbonded pdb=" OG SERH5 48 " pdb=" OD1 ASPH5 52 " model vdw 2.087 2.440 nonbonded pdb=" OG SERH2 48 " pdb=" OD1 ASPH2 52 " model vdw 2.087 2.440 nonbonded pdb=" OG SERH1 48 " pdb=" OD1 ASPH1 52 " model vdw 2.087 2.440 nonbonded pdb=" OG SERH4 48 " pdb=" OD1 ASPH4 52 " model vdw 2.087 2.440 nonbonded pdb=" OG SERH3 48 " pdb=" OD1 ASPH3 52 " model vdw 2.088 2.440 ... (remaining 174350 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 'F1' selection = chain 'F2' selection = chain 'F3' selection = chain 'F4' selection = chain 'F5' } ncs_group { reference = chain 'H1' selection = chain 'H2' selection = chain 'H3' selection = chain 'H4' selection = chain 'H5' } ncs_group { reference = chain 'L1' selection = chain 'L2' selection = chain 'L3' selection = chain 'L4' selection = chain 'L5' } 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: 1.100 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: 0.020 Extract box with map and model: 7.160 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 56.070 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.007 0.063 22225 Z= 0.446 Angle : 0.765 10.199 30290 Z= 0.419 Chirality : 0.047 0.181 3335 Planarity : 0.005 0.063 3905 Dihedral : 17.163 86.487 8130 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.96 % Favored : 88.86 % Rotamer: Outliers : 8.26 % Allowed : 16.32 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.13), residues: 2720 helix: -4.13 (0.17), residues: 125 sheet: -1.40 (0.18), residues: 755 loop : -3.49 (0.11), residues: 1840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 312 time to evaluate : 2.632 Fit side-chains revert: symmetry clash outliers start: 200 outliers final: 110 residues processed: 490 average time/residue: 0.3418 time to fit residues: 256.0673 Evaluate side-chains 386 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 276 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 0 residues processed: 110 average time/residue: 0.2309 time to fit residues: 49.5113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 6 GLN L1 37 GLN H1 69 ASN F1 54 ASN F1 71 GLN F1 80 ASN F1 142 ASN ** F1 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1 254 GLN F1 293 ASN F1 339 GLN F1 347 GLN L2 6 GLN L2 37 GLN H2 69 ASN F2 54 ASN F2 80 ASN F2 142 ASN ** F2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2 254 GLN F2 293 ASN F2 339 GLN F2 347 GLN L3 32 ASN L3 37 GLN L3 92 ASN H3 69 ASN F3 54 ASN F3 80 ASN F3 142 ASN F3 254 GLN F3 293 ASN F3 339 GLN F3 347 GLN L4 32 ASN L4 37 GLN L4 92 ASN H4 69 ASN F4 54 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 80 ASN F4 142 ASN F4 163 HIS ** F4 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 254 GLN F4 293 ASN F4 339 GLN F4 347 GLN L5 37 GLN H5 69 ASN F5 54 ASN F5 71 GLN F5 80 ASN F5 142 ASN ** F5 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 254 GLN F5 293 ASN F5 339 GLN F5 347 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22225 Z= 0.234 Angle : 0.626 8.098 30290 Z= 0.320 Chirality : 0.044 0.144 3335 Planarity : 0.005 0.053 3905 Dihedral : 5.740 21.862 2995 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.39 % Allowed : 20.95 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.15), residues: 2720 helix: -3.12 (0.38), residues: 120 sheet: -0.98 (0.18), residues: 755 loop : -2.81 (0.13), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 343 time to evaluate : 2.897 Fit side-chains outliers start: 82 outliers final: 43 residues processed: 409 average time/residue: 0.2834 time to fit residues: 190.1409 Evaluate side-chains 314 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 271 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2039 time to fit residues: 19.5971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 241 optimal weight: 0.8980 chunk 260 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 32 ASN L1 92 ASN L2 32 ASN L2 92 ASN ** F2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN L5 32 ASN L5 92 ASN F5 92 ASN F5 109 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22225 Z= 0.322 Angle : 0.662 9.562 30290 Z= 0.332 Chirality : 0.045 0.154 3335 Planarity : 0.005 0.052 3905 Dihedral : 5.740 23.792 2995 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.96 % Favored : 90.00 % Rotamer: Outliers : 3.35 % Allowed : 22.60 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.15), residues: 2720 helix: -2.89 (0.38), residues: 120 sheet: -0.80 (0.18), residues: 765 loop : -2.61 (0.13), residues: 1835 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 262 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 53 residues processed: 325 average time/residue: 0.2942 time to fit residues: 155.0421 Evaluate side-chains 309 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.1917 time to fit residues: 22.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 161 optimal weight: 20.0000 chunk 241 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 229 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22225 Z= 0.195 Angle : 0.578 8.148 30290 Z= 0.293 Chirality : 0.043 0.137 3335 Planarity : 0.004 0.045 3905 Dihedral : 5.249 21.294 2995 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.53 % Allowed : 23.88 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2720 helix: -2.47 (0.42), residues: 120 sheet: -0.88 (0.18), residues: 835 loop : -2.30 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 284 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 306 average time/residue: 0.2974 time to fit residues: 148.2554 Evaluate side-chains 274 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 257 time to evaluate : 2.409 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1886 time to fit residues: 9.4409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 40.0000 chunk 145 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 218 optimal weight: 50.0000 chunk 177 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 32 ASN L1 92 ASN F1 92 ASN F1 118 GLN F2 92 ASN ** F2 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 92 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22225 Z= 0.366 Angle : 0.678 11.423 30290 Z= 0.337 Chirality : 0.046 0.159 3335 Planarity : 0.005 0.049 3905 Dihedral : 5.692 24.174 2995 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.15 % Allowed : 24.01 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 2720 helix: -2.31 (0.42), residues: 120 sheet: -0.82 (0.18), residues: 835 loop : -2.24 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 2.522 Fit side-chains outliers start: 52 outliers final: 25 residues processed: 292 average time/residue: 0.3023 time to fit residues: 143.0432 Evaluate side-chains 272 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2037 time to fit residues: 13.2797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 256 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 22 ASN F2 93 ASN F2 228 HIS F3 163 HIS ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22225 Z= 0.186 Angle : 0.576 8.108 30290 Z= 0.292 Chirality : 0.043 0.139 3335 Planarity : 0.004 0.046 3905 Dihedral : 5.151 20.947 2995 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.45 % Allowed : 24.63 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.16), residues: 2720 helix: -1.69 (0.46), residues: 120 sheet: -0.62 (0.18), residues: 835 loop : -2.11 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 257 time to evaluate : 2.466 Fit side-chains outliers start: 35 outliers final: 12 residues processed: 284 average time/residue: 0.3014 time to fit residues: 138.7744 Evaluate side-chains 254 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2673 time to fit residues: 8.7515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 118 GLN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22225 Z= 0.377 Angle : 0.688 11.629 30290 Z= 0.341 Chirality : 0.047 0.160 3335 Planarity : 0.005 0.049 3905 Dihedral : 5.658 23.880 2995 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 1.28 % Allowed : 25.33 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2720 helix: -1.54 (0.49), residues: 120 sheet: -0.63 (0.18), residues: 835 loop : -2.11 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 2.446 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 261 average time/residue: 0.3066 time to fit residues: 130.6403 Evaluate side-chains 257 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.653 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2330 time to fit residues: 10.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 0.0980 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22225 Z= 0.324 Angle : 0.663 10.637 30290 Z= 0.330 Chirality : 0.046 0.148 3335 Planarity : 0.005 0.052 3905 Dihedral : 5.595 23.196 2995 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.03 % Allowed : 25.58 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2720 helix: -1.41 (0.50), residues: 120 sheet: -0.57 (0.18), residues: 835 loop : -2.10 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 2.279 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 255 average time/residue: 0.3143 time to fit residues: 128.7781 Evaluate side-chains 240 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 2.474 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2690 time to fit residues: 7.9365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 0.0030 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 71 GLN F2 93 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22225 Z= 0.195 Angle : 0.591 8.576 30290 Z= 0.298 Chirality : 0.043 0.137 3335 Planarity : 0.004 0.051 3905 Dihedral : 5.180 20.926 2995 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.37 % Allowed : 26.61 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2720 helix: -1.19 (0.51), residues: 120 sheet: -0.43 (0.18), residues: 835 loop : -1.99 (0.15), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 250 time to evaluate : 2.557 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 256 average time/residue: 0.3068 time to fit residues: 127.2223 Evaluate side-chains 245 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2970 time to fit residues: 6.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 264 optimal weight: 0.0040 chunk 242 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 162 optimal weight: 7.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1 53 ASN ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 53 ASN L3 53 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 53 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L5 53 ASN ** F5 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22225 Z= 0.164 Angle : 0.567 7.716 30290 Z= 0.287 Chirality : 0.042 0.138 3335 Planarity : 0.004 0.049 3905 Dihedral : 4.808 20.074 2995 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.31 % Favored : 91.65 % Rotamer: Outliers : 0.12 % Allowed : 26.61 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2720 helix: -1.78 (0.41), residues: 160 sheet: -0.47 (0.17), residues: 900 loop : -1.74 (0.15), residues: 1660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 2.458 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 279 average time/residue: 0.3055 time to fit residues: 138.4598 Evaluate side-chains 253 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1978 time to fit residues: 3.6955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 7.9990 chunk 223 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 31 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L4 32 ASN L4 92 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123062 restraints weight = 22707.373| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.38 r_work: 0.3049 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22225 Z= 0.194 Angle : 0.586 8.575 30290 Z= 0.295 Chirality : 0.043 0.152 3335 Planarity : 0.004 0.057 3905 Dihedral : 4.876 20.680 2995 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.17 % Allowed : 27.48 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2720 helix: -0.86 (0.50), residues: 125 sheet: -0.23 (0.18), residues: 840 loop : -1.69 (0.15), residues: 1755 =============================================================================== Job complete usr+sys time: 4435.06 seconds wall clock time: 81 minutes 34.38 seconds (4894.38 seconds total)