Starting phenix.real_space_refine on Sun Dec 10 09:00:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckz_16707/12_2023/8ckz_16707.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 45 atoms to isotropic. 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 110 5.16 5 C 8780 2.51 5 N 2400 2.21 5 O 2620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13910 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "H" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "J" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "K" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "M" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 579 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 7.79, per 1000 atoms: 0.56 Number of scatterers: 13910 At special positions: 0 Unit cell: (151.59, 153.45, 93, 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 110 16.00 O 2620 8.00 N 2400 7.00 C 8780 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=0, symmetry=0 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 5 sheets defined 76.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 60 removed outlier: 4.139A pdb=" N THR A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.462A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE E 153 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 188 Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 188 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 60 removed outlier: 4.139A pdb=" N THR G 58 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.722A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE H 153 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 176 Processing helix chain 'H' and resid 178 through 188 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.658A pdb=" N ILE H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 219 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 Processing helix chain 'I' and resid 178 through 188 Processing helix chain 'I' and resid 188 through 193 Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR I 200 " --> pdb=" O PRO I 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR J 58 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL J 59 " --> pdb=" O MET J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.462A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.723A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE K 153 " --> pdb=" O ILE K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 176 Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE K 201 " --> pdb=" O ASP K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 176 Processing helix chain 'L' and resid 178 through 188 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.885A pdb=" N THR L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 60 removed outlier: 4.138A pdb=" N THR M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 59 " --> pdb=" O MET M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 84 removed outlier: 3.516A pdb=" N MET M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 175 Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.461A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 removed outlier: 3.723A pdb=" N ILE M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.552A pdb=" N ILE N 153 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 176 Processing helix chain 'N' and resid 178 through 188 Processing helix chain 'N' and resid 188 through 193 Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.657A pdb=" N ILE N 201 " --> pdb=" O ASP N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 176 Processing helix chain 'O' and resid 178 through 188 Processing helix chain 'O' and resid 188 through 193 Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.886A pdb=" N THR O 200 " --> pdb=" O PRO O 196 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'G' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'J' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'M' and resid 2 through 4 875 hydrogen bonds defined for protein. 2550 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: 4.08 Time building geometry restraints manager: 6.03 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: 4590 1.34 - 1.46: 1438 1.46 - 1.57: 7957 1.57 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 14175 Sorted by residual: bond pdb=" N THR N 148 " pdb=" CA THR N 148 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 bond pdb=" N THR I 148 " pdb=" CA THR I 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.29e+00 bond pdb=" N THR O 148 " pdb=" CA THR O 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N THR C 148 " pdb=" CA THR C 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N THR E 148 " pdb=" CA THR E 148 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 ... (remaining 14170 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.75: 610 106.75 - 113.61: 7805 113.61 - 120.47: 5629 120.47 - 127.33: 4981 127.33 - 134.19: 210 Bond angle restraints: 19235 Sorted by residual: angle pdb=" CA LYS G 131 " pdb=" CB LYS G 131 " pdb=" CG LYS G 131 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA LYS M 131 " pdb=" CB LYS M 131 " pdb=" CG LYS M 131 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " pdb=" CG LYS A 131 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C GLU G 175 " pdb=" N GLN G 176 " pdb=" CA GLN G 176 " ideal model delta sigma weight residual 121.18 127.67 -6.49 1.98e+00 2.55e-01 1.08e+01 angle pdb=" C GLU J 175 " pdb=" N GLN J 176 " pdb=" CA GLN J 176 " ideal model delta sigma weight residual 121.18 127.67 -6.49 1.98e+00 2.55e-01 1.08e+01 ... (remaining 19230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8175 17.91 - 35.83: 400 35.83 - 53.74: 105 53.74 - 71.65: 15 71.65 - 89.57: 15 Dihedral angle restraints: 8710 sinusoidal: 3500 harmonic: 5210 Sorted by residual: dihedral pdb=" CA SER D 44 " pdb=" C SER D 44 " pdb=" N GLU D 45 " pdb=" CA GLU D 45 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER J 44 " pdb=" C SER J 44 " pdb=" N GLU J 45 " pdb=" CA GLU J 45 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 44 " pdb=" C SER A 44 " pdb=" N GLU A 45 " pdb=" CA GLU A 45 " ideal model delta harmonic sigma weight residual -180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1223 0.037 - 0.074: 694 0.074 - 0.111: 197 0.111 - 0.149: 64 0.149 - 0.186: 22 Chirality restraints: 2200 Sorted by residual: chirality pdb=" CA GLN N 176 " pdb=" N GLN N 176 " pdb=" C GLN N 176 " pdb=" CB GLN N 176 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA GLN E 176 " pdb=" N GLN E 176 " pdb=" C GLN E 176 " pdb=" CB GLN E 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA GLN B 176 " pdb=" N GLN B 176 " pdb=" C GLN B 176 " pdb=" CB GLN B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 2197 not shown) Planarity restraints: 2485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU M 136 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LEU M 136 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU M 136 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY M 137 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 136 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C LEU D 136 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU D 136 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY D 137 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C LEU A 136 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 136 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 137 " -0.015 2.00e-02 2.50e+03 ... (remaining 2482 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 15 2.55 - 3.14: 11631 3.14 - 3.73: 21836 3.73 - 4.31: 30633 4.31 - 4.90: 50122 Nonbonded interactions: 114237 Sorted by model distance: nonbonded pdb=" CD1 LEU G 20 " pdb=" OE1 GLU J 45 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU D 20 " pdb=" OE1 GLU G 45 " model vdw 1.966 3.460 nonbonded pdb=" OE1 GLU A 45 " pdb=" CD1 LEU M 20 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU A 20 " pdb=" OE1 GLU D 45 " model vdw 1.966 3.460 nonbonded pdb=" CD1 LEU J 20 " pdb=" OE1 GLU M 45 " model vdw 1.966 3.460 ... (remaining 114232 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' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'E' selection = (chain 'F' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'H' selection = (chain 'I' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'K' selection = (chain 'L' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) selection = chain 'N' selection = (chain 'O' and (resid 148 through 157 or (resid 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 221)) } 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 12.470 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 38.290 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.005 0.051 14175 Z= 0.325 Angle : 0.896 6.570 19235 Z= 0.530 Chirality : 0.051 0.186 2200 Planarity : 0.009 0.080 2485 Dihedral : 12.354 89.566 5320 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.16 (0.17), residues: 1760 helix: -1.05 (0.13), residues: 1170 sheet: -2.19 (0.46), residues: 45 loop : 0.57 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP N 184 HIS 0.008 0.004 HIS D 62 PHE 0.019 0.003 PHE J 40 TYR 0.015 0.005 TYR G 130 ARG 0.012 0.002 ARG M 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 1.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.2929 time to fit residues: 197.8179 Evaluate side-chains 385 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 120 HIS D 13 GLN E 219 GLN F 192 GLN G 13 GLN J 13 GLN M 13 GLN N 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14175 Z= 0.211 Angle : 0.574 7.951 19235 Z= 0.297 Chirality : 0.041 0.133 2200 Planarity : 0.004 0.042 2485 Dihedral : 4.613 18.372 1905 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.82 % Allowed : 6.87 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 1760 helix: 0.67 (0.14), residues: 1210 sheet: -1.97 (0.47), residues: 45 loop : 0.98 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 117 HIS 0.004 0.001 HIS A 120 PHE 0.006 0.001 PHE J 32 TYR 0.011 0.001 TYR I 169 ARG 0.006 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 390 time to evaluate : 1.717 Fit side-chains outliers start: 27 outliers final: 19 residues processed: 398 average time/residue: 0.2860 time to fit residues: 159.6687 Evaluate side-chains 377 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1235 time to fit residues: 6.7395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 43 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 192 GLN D 13 GLN E 219 GLN G 13 GLN G 179 GLN H 219 GLN K 219 GLN M 13 GLN N 219 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14175 Z= 0.281 Angle : 0.572 7.401 19235 Z= 0.287 Chirality : 0.042 0.149 2200 Planarity : 0.004 0.048 2485 Dihedral : 4.326 17.674 1905 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.14 % Allowed : 10.03 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.24 (0.19), residues: 1760 helix: 1.01 (0.14), residues: 1210 sheet: -1.64 (0.45), residues: 45 loop : 0.94 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 117 HIS 0.004 0.002 HIS J 120 PHE 0.006 0.001 PHE A 32 TYR 0.012 0.002 TYR I 169 ARG 0.007 0.000 ARG O 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 379 time to evaluate : 1.673 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 380 average time/residue: 0.2835 time to fit residues: 151.3338 Evaluate side-chains 367 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 359 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1192 time to fit residues: 4.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 GLN G 63 GLN G 179 GLN J 13 GLN M 13 GLN N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14175 Z= 0.178 Angle : 0.503 5.925 19235 Z= 0.254 Chirality : 0.040 0.249 2200 Planarity : 0.004 0.048 2485 Dihedral : 3.972 15.699 1905 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.61 (0.19), residues: 1760 helix: 1.32 (0.14), residues: 1215 sheet: -1.48 (0.47), residues: 45 loop : 0.99 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 117 HIS 0.003 0.001 HIS J 120 PHE 0.005 0.001 PHE N 161 TYR 0.010 0.001 TYR C 169 ARG 0.006 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 375 time to evaluate : 1.679 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 378 average time/residue: 0.2808 time to fit residues: 149.6984 Evaluate side-chains 372 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 362 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1251 time to fit residues: 4.7316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN D 13 GLN D 63 GLN E 179 GLN E 183 ASN E 219 GLN J 13 GLN M 13 GLN M 63 GLN N 192 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14175 Z= 0.366 Angle : 0.595 6.763 19235 Z= 0.298 Chirality : 0.043 0.146 2200 Planarity : 0.004 0.050 2485 Dihedral : 4.244 19.429 1905 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.68 % Allowed : 10.64 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.31 (0.19), residues: 1760 helix: 1.13 (0.14), residues: 1210 sheet: -1.35 (0.47), residues: 45 loop : 0.75 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 117 HIS 0.005 0.002 HIS D 120 PHE 0.007 0.001 PHE A 32 TYR 0.012 0.002 TYR O 169 ARG 0.006 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 370 time to evaluate : 1.629 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 377 average time/residue: 0.2828 time to fit residues: 151.3207 Evaluate side-chains 373 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 359 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1170 time to fit residues: 5.1717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 63 GLN J 13 GLN M 13 GLN M 63 GLN N 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14175 Z= 0.234 Angle : 0.532 7.168 19235 Z= 0.268 Chirality : 0.041 0.131 2200 Planarity : 0.004 0.048 2485 Dihedral : 4.048 17.882 1905 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.35 % Allowed : 11.45 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.47 (0.19), residues: 1760 helix: 1.24 (0.14), residues: 1215 sheet: -1.32 (0.50), residues: 45 loop : 0.84 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 117 HIS 0.003 0.001 HIS D 120 PHE 0.005 0.001 PHE G 32 TYR 0.010 0.001 TYR F 169 ARG 0.007 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 372 time to evaluate : 1.753 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 373 average time/residue: 0.2771 time to fit residues: 146.0747 Evaluate side-chains 372 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 359 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1228 time to fit residues: 5.1514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 63 GLN J 13 GLN M 13 GLN M 63 GLN N 192 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14175 Z= 0.203 Angle : 0.526 7.889 19235 Z= 0.264 Chirality : 0.040 0.210 2200 Planarity : 0.004 0.046 2485 Dihedral : 3.989 20.757 1905 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.88 % Allowed : 12.39 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.58 (0.19), residues: 1760 helix: 1.34 (0.15), residues: 1215 sheet: -1.28 (0.51), residues: 45 loop : 0.86 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 117 HIS 0.003 0.001 HIS D 120 PHE 0.005 0.001 PHE M 32 TYR 0.009 0.001 TYR F 169 ARG 0.008 0.000 ARG I 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 366 time to evaluate : 1.897 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 370 average time/residue: 0.2771 time to fit residues: 145.3729 Evaluate side-chains 364 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 358 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1250 time to fit residues: 3.7450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 83 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 0.0070 chunk 153 optimal weight: 0.0010 overall best weight: 0.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 63 GLN M 13 GLN M 63 GLN N 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14175 Z= 0.131 Angle : 0.496 10.188 19235 Z= 0.251 Chirality : 0.039 0.229 2200 Planarity : 0.004 0.043 2485 Dihedral : 3.702 16.617 1905 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.74 % Allowed : 13.13 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.85 (0.19), residues: 1760 helix: 1.52 (0.15), residues: 1220 sheet: -1.28 (0.49), residues: 45 loop : 1.00 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 117 HIS 0.002 0.000 HIS D 84 PHE 0.007 0.001 PHE J 168 TYR 0.009 0.001 TYR B 169 ARG 0.007 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 362 time to evaluate : 1.670 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 363 average time/residue: 0.2846 time to fit residues: 146.9941 Evaluate side-chains 356 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 346 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1291 time to fit residues: 4.8536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 123 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 63 GLN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN G 63 GLN H 176 GLN J 13 GLN M 13 GLN M 63 GLN N 176 GLN N 179 GLN N 183 ASN N 192 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14175 Z= 0.262 Angle : 0.569 8.706 19235 Z= 0.286 Chirality : 0.042 0.252 2200 Planarity : 0.004 0.044 2485 Dihedral : 3.890 17.338 1905 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.47 % Allowed : 13.74 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.69 (0.19), residues: 1760 helix: 1.42 (0.15), residues: 1215 sheet: -1.29 (0.50), residues: 45 loop : 0.90 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 117 HIS 0.003 0.001 HIS G 120 PHE 0.006 0.001 PHE M 32 TYR 0.010 0.001 TYR F 169 ARG 0.007 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 350 time to evaluate : 1.671 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 352 average time/residue: 0.2843 time to fit residues: 144.1193 Evaluate side-chains 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 346 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1355 time to fit residues: 3.1209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 63 GLN D 179 GLN D 183 ASN ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN J 13 GLN M 13 GLN M 63 GLN N 192 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14175 Z= 0.241 Angle : 0.563 8.960 19235 Z= 0.286 Chirality : 0.042 0.241 2200 Planarity : 0.004 0.045 2485 Dihedral : 3.944 16.990 1905 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.47 % Allowed : 14.14 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.58 (0.19), residues: 1760 helix: 1.33 (0.14), residues: 1215 sheet: -1.39 (0.50), residues: 45 loop : 0.86 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 117 HIS 0.003 0.001 HIS G 12 PHE 0.006 0.001 PHE J 32 TYR 0.010 0.001 TYR F 169 ARG 0.008 0.000 ARG N 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 345 time to evaluate : 1.763 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 346 average time/residue: 0.2740 time to fit residues: 135.3592 Evaluate side-chains 346 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 341 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1286 time to fit residues: 3.5625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN D 13 GLN D 63 GLN ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 GLN ** H 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 GLN M 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137374 restraints weight = 17088.534| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.45 r_work: 0.3108 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14175 Z= 0.200 Angle : 0.553 9.156 19235 Z= 0.280 Chirality : 0.041 0.239 2200 Planarity : 0.004 0.047 2485 Dihedral : 3.865 16.355 1905 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.47 % Allowed : 14.41 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.65 (0.19), residues: 1760 helix: 1.37 (0.14), residues: 1220 sheet: -1.40 (0.50), residues: 45 loop : 0.92 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 117 HIS 0.003 0.001 HIS M 12 PHE 0.005 0.001 PHE G 32 TYR 0.009 0.001 TYR B 169 ARG 0.008 0.000 ARG N 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.88 seconds wall clock time: 67 minutes 4.95 seconds (4024.95 seconds total)