Starting phenix.real_space_refine on Sat Feb 17 09:22:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umm_26605/02_2024/7umm_26605_neut.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 69 5.16 5 C 11442 2.51 5 N 3090 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L GLU 169": "OE1" <-> "OE2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 169": "OE1" <-> "OE2" Residue "N ARG 215": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18147 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2707 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 19, 'TRANS': 321} Chain breaks: 1 Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2707 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 19, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2707 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 19, 'TRANS': 321} Chain breaks: 1 Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1614 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1614 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1614 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "L" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1672 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1672 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1672 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.72, per 1000 atoms: 0.48 Number of scatterers: 18147 At special positions: 0 Unit cell: (147.675, 136.125, 155.1, 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 69 16.00 O 3546 8.00 N 3090 7.00 C 11442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 282 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 198 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 198 " distance=2.04 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 62 " " NAG A 602 " - " ASN A 133 " " NAG B 601 " - " ASN B 62 " " NAG B 602 " - " ASN B 133 " " NAG C 601 " - " ASN C 62 " " NAG C 602 " - " ASN C 133 " " NAG D 1 " - " ASN A 95 " " NAG E 1 " - " ASN B 95 " " NAG F 1 " - " ASN C 95 " Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 3.2 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 63 sheets defined 14.5% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.074A pdb=" N SER A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.185A pdb=" N TRP A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 442 Processing helix chain 'B' and resid 64 through 71 Processing helix chain 'B' and resid 105 through 115 removed outlier: 4.074A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 4.184A pdb=" N TRP B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 408 through 442 Processing helix chain 'C' and resid 64 through 71 Processing helix chain 'C' and resid 105 through 115 removed outlier: 4.075A pdb=" N SER C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.184A pdb=" N TRP C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 442 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 158 through 160 No H-bonds generated for 'chain 'H' and resid 158 through 160' Processing helix chain 'H' and resid 203 through 206 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 158 through 160 No H-bonds generated for 'chain 'I' and resid 158 through 160' Processing helix chain 'I' and resid 203 through 206 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 203 through 206 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 125 through 131 removed outlier: 3.708A pdb=" N LEU L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.708A pdb=" N LEU M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 192 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 125 through 131 removed outlier: 3.709A pdb=" N LEU N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.153A pdb=" N LEU A 51 " --> pdb=" O ALA A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.387A pdb=" N LEU A 58 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER A 118 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 183 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER A 118 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS A 143 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 150 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.511A pdb=" N CYS A 286 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.153A pdb=" N LEU B 51 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.388A pdb=" N LEU B 58 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER B 118 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU B 183 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER B 118 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS B 143 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 150 " --> pdb=" O CYS B 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB8, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.511A pdb=" N CYS B 286 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.154A pdb=" N LEU C 51 " --> pdb=" O ALA C 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.388A pdb=" N LEU C 58 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER C 118 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 183 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER C 118 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS C 143 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 150 " --> pdb=" O CYS C 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AC8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.512A pdb=" N CYS C 286 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.576A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N ILE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 153 through 156 removed outlier: 4.073A pdb=" N TYR H 196 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.577A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.696A pdb=" N ILE I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR I 178 " --> pdb=" O ASP I 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR I 178 " --> pdb=" O ASP I 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 153 through 156 removed outlier: 4.072A pdb=" N TYR I 196 " --> pdb=" O VAL I 213 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.576A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N ILE J 110 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR J 178 " --> pdb=" O ASP J 146 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR J 178 " --> pdb=" O ASP J 146 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 153 through 156 removed outlier: 4.073A pdb=" N TYR J 196 " --> pdb=" O VAL J 213 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.111A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AF4, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.708A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR L 53 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER L 135 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU L 185 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL L 137 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU L 183 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU L 139 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER L 181 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN L 141 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU L 179 " --> pdb=" O ASN L 141 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.146A pdb=" N TRP L 152 " --> pdb=" O GLN L 159 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.110A pdb=" N LEU M 11 " --> pdb=" O GLU M 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'M' and resid 30 through 31 Processing sheet with id=AG1, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.707A pdb=" N TRP M 39 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE M 37 " --> pdb=" O TYR M 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER M 135 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU M 185 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL M 137 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU M 183 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU M 139 " --> pdb=" O SER M 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER M 181 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN M 141 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU M 179 " --> pdb=" O ASN M 141 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 157 through 159 removed outlier: 4.145A pdb=" N TRP M 152 " --> pdb=" O GLN M 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.111A pdb=" N LEU N 11 " --> pdb=" O GLU N 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AG7, first strand: chain 'N' and resid 57 through 58 removed outlier: 6.708A pdb=" N TRP N 39 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR N 53 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE N 37 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER N 135 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU N 185 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL N 137 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU N 183 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU N 139 " --> pdb=" O SER N 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER N 181 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN N 141 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU N 179 " --> pdb=" O ASN N 141 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 157 through 159 removed outlier: 4.146A pdb=" N TRP N 152 " --> pdb=" O GLN N 159 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 1854 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: 7.17 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5529 1.33 - 1.45: 3746 1.45 - 1.57: 9223 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 18588 Sorted by residual: bond pdb=" C ILE B 55 " pdb=" N ALA B 56 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.07e-02 2.33e+03 1.48e+01 bond pdb=" C ILE A 55 " pdb=" N ALA A 56 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.07e-02 2.33e+03 1.48e+01 bond pdb=" C ILE C 55 " pdb=" N ALA C 56 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.47e+01 bond pdb=" C MET B 411 " pdb=" O MET B 411 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.21e-02 6.83e+03 1.43e+01 bond pdb=" C MET A 411 " pdb=" O MET A 411 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.21e-02 6.83e+03 1.42e+01 ... (remaining 18583 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.42: 360 104.42 - 111.82: 9036 111.82 - 119.22: 6053 119.22 - 126.62: 9522 126.62 - 134.02: 313 Bond angle restraints: 25284 Sorted by residual: angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 125.89 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB MET J 81 " pdb=" CG MET J 81 " pdb=" SD MET J 81 " ideal model delta sigma weight residual 112.70 125.88 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 125.87 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" N ARG N 215 " pdb=" CA ARG N 215 " pdb=" C ARG N 215 " ideal model delta sigma weight residual 109.96 114.87 -4.91 1.49e+00 4.50e-01 1.09e+01 angle pdb=" N ARG L 215 " pdb=" CA ARG L 215 " pdb=" C ARG L 215 " ideal model delta sigma weight residual 109.96 114.84 -4.88 1.49e+00 4.50e-01 1.07e+01 ... (remaining 25279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 10368 18.03 - 36.07: 732 36.07 - 54.10: 132 54.10 - 72.14: 27 72.14 - 90.17: 15 Dihedral angle restraints: 11274 sinusoidal: 4569 harmonic: 6705 Sorted by residual: dihedral pdb=" CA MET B 279 " pdb=" C MET B 279 " pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET C 279 " pdb=" C MET C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET A 279 " pdb=" C MET A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2624 0.101 - 0.202: 199 0.202 - 0.303: 0 0.303 - 0.404: 3 0.404 - 0.505: 3 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CG LEU C 240 " pdb=" CB LEU C 240 " pdb=" CD1 LEU C 240 " pdb=" CD2 LEU C 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 2826 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 165 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 166 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 165 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 166 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 165 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 166 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.030 5.00e-02 4.00e+02 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 477 2.66 - 3.22: 18316 3.22 - 3.78: 29036 3.78 - 4.34: 40306 4.34 - 4.90: 67183 Nonbonded interactions: 155318 Sorted by model distance: nonbonded pdb=" O THR C 136 " pdb=" OG1 THR C 137 " model vdw 2.096 2.440 nonbonded pdb=" O THR A 136 " pdb=" OG1 THR A 137 " model vdw 2.097 2.440 nonbonded pdb=" O THR B 136 " pdb=" OG1 THR B 137 " model vdw 2.098 2.440 nonbonded pdb=" O3 NAG F 2 " pdb=" O7 NAG F 2 " model vdw 2.127 2.440 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.127 2.440 ... (remaining 155313 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.720 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 50.300 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.014 0.131 18588 Z= 0.906 Angle : 0.824 13.185 25284 Z= 0.446 Chirality : 0.058 0.505 2829 Planarity : 0.005 0.055 3249 Dihedral : 13.077 90.173 6912 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 0.30 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -2.00 (0.16), residues: 2298 helix: -2.41 (0.27), residues: 216 sheet: -0.63 (0.18), residues: 810 loop : -1.59 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 50 HIS 0.017 0.002 HIS C 212 PHE 0.027 0.002 PHE A 119 TYR 0.018 0.002 TYR I 95 ARG 0.011 0.001 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 284 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 CYS cc_start: 0.6385 (m) cc_final: 0.6066 (m) REVERT: A 411 MET cc_start: 0.7604 (mmt) cc_final: 0.6951 (mmt) REVERT: B 50 CYS cc_start: 0.6435 (m) cc_final: 0.6156 (m) REVERT: B 424 ASP cc_start: 0.7349 (m-30) cc_final: 0.7146 (m-30) REVERT: C 50 CYS cc_start: 0.6400 (m) cc_final: 0.6123 (m) REVERT: C 411 MET cc_start: 0.7646 (mmt) cc_final: 0.6861 (mmt) REVERT: C 424 ASP cc_start: 0.7360 (m-30) cc_final: 0.7142 (m-30) REVERT: I 156 TRP cc_start: 0.8475 (m100) cc_final: 0.8038 (m100) REVERT: J 156 TRP cc_start: 0.8519 (m100) cc_final: 0.8312 (m100) REVERT: M 149 LYS cc_start: 0.7731 (tttp) cc_final: 0.7429 (mmmt) outliers start: 9 outliers final: 3 residues processed: 287 average time/residue: 0.3069 time to fit residues: 132.6468 Evaluate side-chains 205 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain C residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 59 GLN C 287 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18588 Z= 0.220 Angle : 0.637 10.129 25284 Z= 0.328 Chirality : 0.047 0.270 2829 Planarity : 0.005 0.037 3249 Dihedral : 6.888 59.910 2763 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.90 % Allowed : 8.13 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.74 (0.17), residues: 2298 helix: 0.56 (0.32), residues: 222 sheet: -0.02 (0.18), residues: 789 loop : -0.97 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 152 HIS 0.006 0.001 HIS B 303 PHE 0.016 0.002 PHE C 119 TYR 0.016 0.002 TYR N 144 ARG 0.005 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 CYS cc_start: 0.6337 (m) cc_final: 0.6134 (m) REVERT: B 280 ASP cc_start: 0.5976 (m-30) cc_final: 0.5738 (m-30) REVERT: B 283 ASP cc_start: 0.7983 (t70) cc_final: 0.7676 (t0) REVERT: C 50 CYS cc_start: 0.6256 (m) cc_final: 0.6037 (m) REVERT: C 283 ASP cc_start: 0.8138 (t70) cc_final: 0.7733 (t0) REVERT: C 420 ASP cc_start: 0.6847 (t0) cc_final: 0.6574 (t0) REVERT: H 156 TRP cc_start: 0.8437 (m100) cc_final: 0.8070 (m100) REVERT: I 125 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7404 (tmtt) REVERT: I 156 TRP cc_start: 0.8443 (m100) cc_final: 0.8050 (m100) REVERT: J 125 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7394 (tmtt) REVERT: J 156 TRP cc_start: 0.8505 (m100) cc_final: 0.8249 (m100) outliers start: 18 outliers final: 13 residues processed: 258 average time/residue: 0.3220 time to fit residues: 123.8138 Evaluate side-chains 205 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 199 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 57 optimal weight: 0.0060 chunk 207 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 overall best weight: 4.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 18588 Z= 0.486 Angle : 0.718 10.628 25284 Z= 0.359 Chirality : 0.050 0.248 2829 Planarity : 0.005 0.044 3249 Dihedral : 7.206 59.171 2761 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.81 % Allowed : 10.04 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.78 (0.17), residues: 2298 helix: 0.73 (0.34), residues: 222 sheet: -0.07 (0.18), residues: 789 loop : -1.03 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 50 HIS 0.009 0.002 HIS L 202 PHE 0.017 0.002 PHE M 122 TYR 0.017 0.002 TYR M 90 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.7530 (mmt) cc_final: 0.7160 (mmt) REVERT: B 41 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7961 (tp) REVERT: H 156 TRP cc_start: 0.8517 (m100) cc_final: 0.8161 (m100) REVERT: I 156 TRP cc_start: 0.8492 (m100) cc_final: 0.8092 (m100) outliers start: 36 outliers final: 25 residues processed: 237 average time/residue: 0.3414 time to fit residues: 117.5294 Evaluate side-chains 215 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 415 ASN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18588 Z= 0.172 Angle : 0.566 8.194 25284 Z= 0.288 Chirality : 0.044 0.273 2829 Planarity : 0.004 0.043 3249 Dihedral : 6.528 58.594 2761 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.71 % Allowed : 11.40 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.44 (0.17), residues: 2298 helix: 1.29 (0.35), residues: 222 sheet: 0.10 (0.18), residues: 789 loop : -0.81 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 152 HIS 0.006 0.001 HIS L 202 PHE 0.015 0.001 PHE A 119 TYR 0.015 0.001 TYR J 147 ARG 0.005 0.000 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 SER cc_start: 0.7278 (t) cc_final: 0.7065 (p) REVERT: C 411 MET cc_start: 0.8412 (mmt) cc_final: 0.8078 (mmt) REVERT: H 156 TRP cc_start: 0.8449 (m100) cc_final: 0.8159 (m100) REVERT: H 211 LYS cc_start: 0.7770 (tppp) cc_final: 0.7536 (ttmm) REVERT: I 81 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (ttp) REVERT: I 156 TRP cc_start: 0.8470 (m100) cc_final: 0.8048 (m100) REVERT: I 211 LYS cc_start: 0.7735 (tppp) cc_final: 0.7475 (ttmm) REVERT: L 11 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8102 (mm) REVERT: N 11 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8021 (mm) outliers start: 34 outliers final: 20 residues processed: 257 average time/residue: 0.3139 time to fit residues: 119.7246 Evaluate side-chains 219 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 415 ASN B 59 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN M 128 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18588 Z= 0.249 Angle : 0.575 8.016 25284 Z= 0.289 Chirality : 0.045 0.250 2829 Planarity : 0.004 0.047 3249 Dihedral : 6.410 58.287 2761 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 12.95 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.33 (0.17), residues: 2298 helix: 1.33 (0.35), residues: 222 sheet: 0.19 (0.18), residues: 789 loop : -0.74 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 152 HIS 0.008 0.001 HIS M 202 PHE 0.013 0.002 PHE A 119 TYR 0.013 0.001 TYR N 144 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8135 (mmt) cc_final: 0.7935 (mmt) REVERT: H 156 TRP cc_start: 0.8431 (m100) cc_final: 0.8131 (m100) REVERT: H 211 LYS cc_start: 0.7730 (tppp) cc_final: 0.7491 (ttmm) REVERT: I 81 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8304 (ttp) REVERT: I 156 TRP cc_start: 0.8444 (m100) cc_final: 0.8009 (m100) REVERT: I 211 LYS cc_start: 0.7663 (tppp) cc_final: 0.7399 (ttmm) REVERT: L 11 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8096 (mm) REVERT: N 11 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7979 (mm) outliers start: 35 outliers final: 28 residues processed: 246 average time/residue: 0.3266 time to fit residues: 118.1930 Evaluate side-chains 233 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN I 199 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18588 Z= 0.294 Angle : 0.588 8.018 25284 Z= 0.295 Chirality : 0.045 0.248 2829 Planarity : 0.005 0.046 3249 Dihedral : 6.464 58.828 2761 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.06 % Allowed : 13.65 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2298 helix: 1.27 (0.35), residues: 222 sheet: 0.21 (0.18), residues: 789 loop : -0.70 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 152 HIS 0.006 0.001 HIS L 202 PHE 0.013 0.002 PHE A 119 TYR 0.017 0.002 TYR N 144 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 156 TRP cc_start: 0.8456 (m100) cc_final: 0.8170 (m100) REVERT: I 81 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (ttp) REVERT: I 156 TRP cc_start: 0.8447 (m100) cc_final: 0.8069 (m100) REVERT: L 11 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8121 (mm) REVERT: N 11 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7989 (mm) outliers start: 41 outliers final: 28 residues processed: 247 average time/residue: 0.3347 time to fit residues: 121.8943 Evaluate side-chains 233 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 415 ASN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18588 Z= 0.241 Angle : 0.567 8.040 25284 Z= 0.285 Chirality : 0.044 0.246 2829 Planarity : 0.004 0.047 3249 Dihedral : 6.354 58.255 2761 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.96 % Allowed : 14.06 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.29 (0.17), residues: 2298 helix: 1.29 (0.35), residues: 222 sheet: 0.09 (0.18), residues: 819 loop : -0.61 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 152 HIS 0.012 0.001 HIS M 202 PHE 0.012 0.001 PHE M 120 TYR 0.019 0.001 TYR N 144 ARG 0.008 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 268 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.7079 (p90) REVERT: H 156 TRP cc_start: 0.8455 (m100) cc_final: 0.8136 (m100) REVERT: I 81 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8253 (ttp) REVERT: I 156 TRP cc_start: 0.8446 (m100) cc_final: 0.8094 (m100) REVERT: L 11 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8139 (mm) REVERT: L 18 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7475 (ttm110) REVERT: M 205 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4755 (mt) REVERT: N 4 MET cc_start: 0.8346 (tpp) cc_final: 0.8129 (tpp) REVERT: N 11 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7959 (mm) REVERT: N 147 GLU cc_start: 0.7601 (mp0) cc_final: 0.7366 (mp0) REVERT: N 189 ASP cc_start: 0.7737 (t0) cc_final: 0.7429 (t0) outliers start: 39 outliers final: 28 residues processed: 237 average time/residue: 0.3259 time to fit residues: 114.0554 Evaluate side-chains 231 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.0050 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18588 Z= 0.158 Angle : 0.537 7.908 25284 Z= 0.271 Chirality : 0.043 0.244 2829 Planarity : 0.004 0.047 3249 Dihedral : 5.977 55.903 2761 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.86 % Allowed : 14.56 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.11 (0.18), residues: 2298 helix: 1.55 (0.36), residues: 222 sheet: 0.22 (0.18), residues: 819 loop : -0.52 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 152 HIS 0.010 0.001 HIS M 202 PHE 0.013 0.001 PHE M 120 TYR 0.018 0.001 TYR N 144 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7609 (mttt) REVERT: B 226 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7546 (mttt) REVERT: H 156 TRP cc_start: 0.8458 (m100) cc_final: 0.8097 (m100) REVERT: L 11 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8239 (mm) REVERT: L 18 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7524 (ttm110) REVERT: N 11 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7990 (mm) REVERT: N 147 GLU cc_start: 0.7561 (mp0) cc_final: 0.7315 (mp0) REVERT: N 189 ASP cc_start: 0.7623 (t0) cc_final: 0.7345 (t0) outliers start: 37 outliers final: 24 residues processed: 254 average time/residue: 0.3303 time to fit residues: 123.4076 Evaluate side-chains 237 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 65 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 ASN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18588 Z= 0.172 Angle : 0.549 8.799 25284 Z= 0.275 Chirality : 0.043 0.230 2829 Planarity : 0.004 0.048 3249 Dihedral : 5.842 55.473 2761 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.51 % Allowed : 14.96 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.02 (0.18), residues: 2298 helix: 1.59 (0.36), residues: 222 sheet: 0.29 (0.18), residues: 822 loop : -0.47 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 152 HIS 0.013 0.001 HIS M 202 PHE 0.012 0.001 PHE B 119 TYR 0.018 0.001 TYR N 144 ARG 0.009 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7585 (mttt) REVERT: B 226 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7454 (mttm) REVERT: H 156 TRP cc_start: 0.8459 (m100) cc_final: 0.8100 (m100) REVERT: L 11 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8244 (mm) REVERT: N 11 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7987 (mm) REVERT: N 147 GLU cc_start: 0.7649 (mp0) cc_final: 0.7398 (mp0) REVERT: N 189 ASP cc_start: 0.7520 (t0) cc_final: 0.7243 (t0) outliers start: 30 outliers final: 24 residues processed: 244 average time/residue: 0.3348 time to fit residues: 120.5449 Evaluate side-chains 239 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.0870 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 143 optimal weight: 0.0980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 43 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18588 Z= 0.174 Angle : 0.553 8.784 25284 Z= 0.278 Chirality : 0.043 0.225 2829 Planarity : 0.004 0.055 3249 Dihedral : 5.757 54.895 2761 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.51 % Allowed : 15.01 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.01 (0.18), residues: 2298 helix: 1.50 (0.36), residues: 222 sheet: 0.32 (0.18), residues: 828 loop : -0.43 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 152 HIS 0.013 0.001 HIS M 202 PHE 0.012 0.001 PHE M 120 TYR 0.018 0.001 TYR N 144 ARG 0.011 0.000 ARG M 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7572 (mttt) REVERT: B 226 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7459 (mttm) REVERT: H 156 TRP cc_start: 0.8472 (m100) cc_final: 0.8097 (m100) REVERT: I 131 PRO cc_start: 0.5837 (Cg_endo) cc_final: 0.5554 (Cg_exo) REVERT: L 11 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8303 (mm) REVERT: L 18 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7526 (ttm110) REVERT: N 11 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8012 (mm) REVERT: N 147 GLU cc_start: 0.7633 (mp0) cc_final: 0.7376 (mp0) REVERT: N 189 ASP cc_start: 0.7490 (t0) cc_final: 0.7239 (t0) outliers start: 30 outliers final: 25 residues processed: 242 average time/residue: 0.3245 time to fit residues: 115.8097 Evaluate side-chains 240 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** H 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 ASN J 43 GLN ** J 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.115797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085145 restraints weight = 32156.465| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.47 r_work: 0.2890 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18588 Z= 0.264 Angle : 0.587 10.179 25284 Z= 0.293 Chirality : 0.045 0.223 2829 Planarity : 0.005 0.063 3249 Dihedral : 5.933 56.292 2761 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.46 % Allowed : 15.06 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: -0.04 (0.18), residues: 2298 helix: 1.33 (0.36), residues: 222 sheet: 0.32 (0.18), residues: 828 loop : -0.47 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 152 HIS 0.011 0.001 HIS M 202 PHE 0.012 0.001 PHE M 120 TYR 0.019 0.002 TYR N 144 ARG 0.009 0.000 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4147.57 seconds wall clock time: 76 minutes 30.17 seconds (4590.17 seconds total)