Starting phenix.real_space_refine on Sun Feb 18 09:17:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3a_22654/02_2024/7k3a_22654.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 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 99 5.16 5 C 13359 2.51 5 N 3618 2.21 5 O 4350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21426 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1353 Classifications: {'peptide': 165} Link IDs: {'TRANS': 164} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.71, per 1000 atoms: 0.64 Number of scatterers: 21426 At special positions: 0 Unit cell: (183.54, 183.54, 144.97, 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 99 16.00 O 4350 8.00 N 3618 7.00 C 13359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.32 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.83 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.93 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG F 301 " - " ASN F 154 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 8.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 19.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 38 through 50 removed outlier: 4.322A pdb=" N GLY B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.323A pdb=" N GLY D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.246A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 38 through 50 removed outlier: 4.322A pdb=" N GLY F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.517A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 197 through 202 Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.516A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 197 through 202 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.516A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 197 through 202 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.830A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.553A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.135A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.953A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.555A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.134A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 33 through 37 removed outlier: 4.829A pdb=" N TYR F 22 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY E 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.768A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.952A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.554A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.133A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.193A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 5.659A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.135A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.317A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.090A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 160 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.372A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.557A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.090A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N SER J 187 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA J 178 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER J 189 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 160 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.607A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.978A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 159 removed outlier: 3.999A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.318A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.091A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 187 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA L 178 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER L 189 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 160 through 164 921 hydrogen bonds defined for protein. 2346 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: 7.37 Time building geometry restraints manager: 9.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6898 1.35 - 1.47: 5629 1.47 - 1.60: 9205 1.60 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 21870 Sorted by residual: bond pdb=" C1 MAN U 4 " pdb=" C2 MAN U 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.490 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 21865 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.65: 748 106.65 - 113.51: 12538 113.51 - 120.36: 7367 120.36 - 127.22: 8781 127.22 - 134.08: 266 Bond angle restraints: 29700 Sorted by residual: angle pdb=" CA VAL J 194 " pdb=" C VAL J 194 " pdb=" N PRO J 195 " ideal model delta sigma weight residual 116.57 120.04 -3.47 9.80e-01 1.04e+00 1.26e+01 angle pdb=" CA VAL L 194 " pdb=" C VAL L 194 " pdb=" N PRO L 195 " ideal model delta sigma weight residual 116.57 120.01 -3.44 9.80e-01 1.04e+00 1.23e+01 angle pdb=" CA VAL H 194 " pdb=" C VAL H 194 " pdb=" N PRO H 195 " ideal model delta sigma weight residual 116.57 119.98 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" C VAL J 194 " pdb=" CA VAL J 194 " pdb=" CB VAL J 194 " ideal model delta sigma weight residual 109.33 112.39 -3.06 9.80e-01 1.04e+00 9.78e+00 angle pdb=" C VAL H 194 " pdb=" CA VAL H 194 " pdb=" CB VAL H 194 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.68e+00 ... (remaining 29695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 12868 21.98 - 43.97: 734 43.97 - 65.95: 102 65.95 - 87.93: 48 87.93 - 109.91: 24 Dihedral angle restraints: 13776 sinusoidal: 6069 harmonic: 7707 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 42.08 50.92 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 47.87 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CA CYS E 14 " pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " ideal model delta sinusoidal sigma weight residual -73.00 -0.71 -72.29 1 2.00e+01 2.50e-03 1.67e+01 ... (remaining 13773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3051 0.079 - 0.159: 394 0.159 - 0.238: 23 0.238 - 0.317: 15 0.317 - 0.397: 3 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C3 MAN O 4 " pdb=" C2 MAN O 4 " pdb=" C4 MAN O 4 " pdb=" O3 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C3 MAN U 4 " pdb=" C2 MAN U 4 " pdb=" C4 MAN U 4 " pdb=" O3 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C3 MAN R 4 " pdb=" C2 MAN R 4 " pdb=" C4 MAN R 4 " pdb=" O3 MAN R 4 " both_signs ideal model delta sigma weight residual False 2.47 2.08 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 3483 not shown) Planarity restraints: 3771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 178 " -0.006 2.00e-02 2.50e+03 1.40e-02 3.90e+00 pdb=" CG TYR I 178 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR I 178 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR I 178 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR I 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR I 178 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 178 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 178 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 220 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO A 221 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 220 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 221 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.021 5.00e-02 4.00e+02 ... (remaining 3768 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 316 2.62 - 3.19: 18968 3.19 - 3.76: 33629 3.76 - 4.33: 48357 4.33 - 4.90: 78252 Nonbonded interactions: 179522 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.053 2.440 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.124 2.520 nonbonded pdb=" O GLY K 24 " pdb=" OG1 THR K 71 " model vdw 2.128 2.440 nonbonded pdb=" OE1 GLN C 210 " pdb=" NE ARG E 220 " model vdw 2.145 2.520 nonbonded pdb=" O TYR I 191 " pdb=" OH TYR I 197 " model vdw 2.164 2.440 ... (remaining 179517 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.820 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 59.950 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.004 0.051 21870 Z= 0.283 Angle : 0.818 8.594 29700 Z= 0.422 Chirality : 0.054 0.397 3486 Planarity : 0.005 0.038 3753 Dihedral : 14.882 109.914 8754 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.17 % Allowed : 0.60 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.62 (0.16), residues: 2649 helix: 1.75 (0.26), residues: 384 sheet: -0.20 (0.17), residues: 867 loop : -1.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 50 HIS 0.006 0.001 HIS F 159 PHE 0.019 0.002 PHE I 123 TYR 0.030 0.002 TYR I 178 ARG 0.008 0.001 ARG G 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 498 time to evaluate : 2.488 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7617 (mmm) cc_final: 0.5942 (mmt) REVERT: A 233 TYR cc_start: 0.7243 (m-80) cc_final: 0.7014 (m-10) REVERT: B 73 VAL cc_start: 0.9090 (t) cc_final: 0.8761 (t) REVERT: B 80 LEU cc_start: 0.9427 (tp) cc_final: 0.8812 (tt) REVERT: B 161 VAL cc_start: 0.8221 (m) cc_final: 0.7689 (p) REVERT: C 316 LEU cc_start: 0.7963 (tp) cc_final: 0.7724 (tt) REVERT: D 81 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7568 (mt-10) REVERT: D 89 ILE cc_start: 0.9117 (mt) cc_final: 0.7105 (mt) REVERT: D 94 TYR cc_start: 0.7837 (t80) cc_final: 0.7505 (t80) REVERT: D 95 ASN cc_start: 0.8553 (m-40) cc_final: 0.8238 (m110) REVERT: F 80 LEU cc_start: 0.9427 (tp) cc_final: 0.9205 (tp) REVERT: F 171 PHE cc_start: 0.6141 (m-10) cc_final: 0.5919 (m-10) REVERT: G 143 ASN cc_start: 0.8240 (m110) cc_final: 0.7745 (p0) REVERT: G 159 LEU cc_start: 0.7708 (tp) cc_final: 0.7459 (tt) REVERT: H 121 MET cc_start: 0.8576 (tpt) cc_final: 0.8107 (tpt) REVERT: I 191 TYR cc_start: 0.7706 (t80) cc_final: 0.7425 (t80) REVERT: J 98 ARG cc_start: 0.8142 (ttp-170) cc_final: 0.7869 (ttp-170) REVERT: J 164 TRP cc_start: 0.6005 (m100) cc_final: 0.5792 (m100) REVERT: K 143 ASN cc_start: 0.8374 (m-40) cc_final: 0.7534 (p0) REVERT: K 174 LYS cc_start: 0.7940 (pttt) cc_final: 0.7654 (tptp) outliers start: 4 outliers final: 0 residues processed: 502 average time/residue: 0.4401 time to fit residues: 309.6991 Evaluate side-chains 210 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 0.0070 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 106 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS E 189 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 21870 Z= 0.523 Angle : 0.880 10.337 29700 Z= 0.443 Chirality : 0.051 0.304 3486 Planarity : 0.006 0.066 3753 Dihedral : 10.825 77.280 3960 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.71 (0.16), residues: 2649 helix: 1.34 (0.24), residues: 384 sheet: -0.07 (0.18), residues: 789 loop : -1.20 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 153 HIS 0.014 0.003 HIS F 142 PHE 0.027 0.003 PHE J 176 TYR 0.021 0.003 TYR C 233 ARG 0.009 0.001 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 2.507 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: 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: 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 82 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 17 MET cc_start: 0.2074 (ttm) cc_final: 0.1794 (ttp) REVERT: D 95 ASN cc_start: 0.8567 (m-40) cc_final: 0.8251 (m110) REVERT: F 17 MET cc_start: 0.1685 (mtm) cc_final: 0.1343 (mtm) REVERT: G 143 ASN cc_start: 0.8607 (m-40) cc_final: 0.7915 (p0) REVERT: G 159 LEU cc_start: 0.7184 (tp) cc_final: 0.6956 (tt) REVERT: K 143 ASN cc_start: 0.8442 (m-40) cc_final: 0.7268 (p0) REVERT: K 174 LYS cc_start: 0.8272 (pttt) cc_final: 0.7812 (tptp) REVERT: L 148 LEU cc_start: 0.7607 (mt) cc_final: 0.7159 (pt) outliers start: 2 outliers final: 1 residues processed: 255 average time/residue: 0.4073 time to fit residues: 150.4972 Evaluate side-chains 161 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 213 optimal weight: 0.0970 chunk 238 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 189 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN F 106 HIS ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21870 Z= 0.244 Angle : 0.646 9.698 29700 Z= 0.325 Chirality : 0.047 0.303 3486 Planarity : 0.004 0.046 3753 Dihedral : 9.898 71.857 3960 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.52 (0.16), residues: 2649 helix: 1.75 (0.25), residues: 384 sheet: -0.06 (0.18), residues: 783 loop : -1.09 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 153 HIS 0.011 0.001 HIS B 159 PHE 0.020 0.002 PHE L 176 TYR 0.017 0.002 TYR K 191 ARG 0.006 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.586 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: 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: symmetry clash REVERT: A 27 LYS cc_start: 0.6542 (mptt) cc_final: 0.6272 (mptt) REVERT: F 161 VAL cc_start: 0.7634 (m) cc_final: 0.7316 (p) REVERT: G 143 ASN cc_start: 0.8461 (m-40) cc_final: 0.7719 (p0) REVERT: I 143 ASN cc_start: 0.8268 (m-40) cc_final: 0.7117 (p0) REVERT: I 191 TYR cc_start: 0.8013 (t80) cc_final: 0.7683 (t80) REVERT: J 164 TRP cc_start: 0.6253 (m100) cc_final: 0.5810 (m100) REVERT: J 218 ASP cc_start: 0.7715 (m-30) cc_final: 0.7022 (m-30) REVERT: K 17 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7099 (ttp80) REVERT: K 143 ASN cc_start: 0.8444 (m-40) cc_final: 0.7388 (p0) REVERT: L 148 LEU cc_start: 0.7570 (mt) cc_final: 0.7236 (pt) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.4208 time to fit residues: 153.3537 Evaluate side-chains 163 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 161 optimal weight: 0.0170 chunk 241 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN B 159 HIS C 189 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN E 44 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 GLN ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 21870 Z= 0.447 Angle : 0.806 11.625 29700 Z= 0.404 Chirality : 0.049 0.325 3486 Planarity : 0.006 0.058 3753 Dihedral : 9.544 67.506 3960 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 0.13 % Allowed : 5.67 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.94 (0.16), residues: 2649 helix: 0.89 (0.25), residues: 402 sheet: -0.16 (0.18), residues: 765 loop : -1.33 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 37 HIS 0.006 0.001 HIS G 36 PHE 0.022 0.003 PHE L 132 TYR 0.023 0.002 TYR K 191 ARG 0.016 0.001 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 2.760 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: symmetry clash revert: symmetry clash REVERT: A 311 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8892 (mp10) REVERT: G 143 ASN cc_start: 0.8553 (m-40) cc_final: 0.7536 (p0) REVERT: H 121 MET cc_start: 0.8697 (tpt) cc_final: 0.8429 (tpt) REVERT: H 154 ASP cc_start: 0.7939 (m-30) cc_final: 0.7669 (m-30) REVERT: H 218 ASP cc_start: 0.8652 (m-30) cc_final: 0.8153 (m-30) REVERT: I 143 ASN cc_start: 0.8410 (m-40) cc_final: 0.7151 (p0) REVERT: I 191 TYR cc_start: 0.8159 (t80) cc_final: 0.7839 (t80) REVERT: J 106 MET cc_start: 0.9253 (mtm) cc_final: 0.9015 (mtm) REVERT: J 154 ASP cc_start: 0.7977 (m-30) cc_final: 0.7737 (m-30) REVERT: J 218 ASP cc_start: 0.8283 (m-30) cc_final: 0.7743 (m-30) REVERT: K 143 ASN cc_start: 0.8401 (m-40) cc_final: 0.7239 (p0) REVERT: L 121 MET cc_start: 0.8760 (tpt) cc_final: 0.8399 (tpt) outliers start: 3 outliers final: 1 residues processed: 202 average time/residue: 0.3925 time to fit residues: 118.0648 Evaluate side-chains 141 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 GLN ** I 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21870 Z= 0.263 Angle : 0.661 9.778 29700 Z= 0.332 Chirality : 0.048 0.356 3486 Planarity : 0.005 0.062 3753 Dihedral : 8.799 62.224 3960 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.04 % Allowed : 1.93 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.72 (0.16), residues: 2649 helix: 1.08 (0.25), residues: 402 sheet: -0.20 (0.18), residues: 843 loop : -1.11 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 153 HIS 0.008 0.001 HIS F 159 PHE 0.019 0.002 PHE F 171 TYR 0.020 0.002 TYR K 191 ARG 0.009 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 2.537 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: symmetry clash revert: symmetry clash REVERT: B 76 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7594 (ttt-90) REVERT: D 17 MET cc_start: -0.0161 (mtm) cc_final: -0.0472 (mtp) REVERT: F 40 SER cc_start: 0.9277 (p) cc_final: 0.9058 (p) REVERT: G 143 ASN cc_start: 0.8452 (m-40) cc_final: 0.7466 (p0) REVERT: G 191 TYR cc_start: 0.8498 (t80) cc_final: 0.8168 (t80) REVERT: H 121 MET cc_start: 0.8573 (tpt) cc_final: 0.8284 (tpt) REVERT: H 154 ASP cc_start: 0.7953 (m-30) cc_final: 0.7648 (m-30) REVERT: I 143 ASN cc_start: 0.8264 (m-40) cc_final: 0.7106 (p0) REVERT: I 191 TYR cc_start: 0.8099 (t80) cc_final: 0.7777 (t80) REVERT: J 10 GLU cc_start: 0.8177 (tp30) cc_final: 0.7797 (tm-30) REVERT: J 121 MET cc_start: 0.8623 (tpt) cc_final: 0.8333 (tpt) REVERT: J 218 ASP cc_start: 0.7696 (m-30) cc_final: 0.6681 (m-30) REVERT: K 143 ASN cc_start: 0.8190 (m-40) cc_final: 0.7210 (p0) REVERT: L 121 MET cc_start: 0.8691 (tpt) cc_final: 0.8482 (tpt) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.3740 time to fit residues: 120.3588 Evaluate side-chains 147 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21870 Z= 0.412 Angle : 0.764 10.747 29700 Z= 0.383 Chirality : 0.049 0.286 3486 Planarity : 0.005 0.059 3753 Dihedral : 9.018 64.519 3960 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2649 helix: 0.77 (0.25), residues: 399 sheet: -0.34 (0.18), residues: 807 loop : -1.35 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 222 HIS 0.006 0.001 HIS F 159 PHE 0.025 0.002 PHE L 132 TYR 0.022 0.002 TYR F 83 ARG 0.009 0.001 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 2.441 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: G 159 LEU cc_start: 0.7361 (tp) cc_final: 0.7141 (tp) REVERT: H 121 MET cc_start: 0.8563 (tpt) cc_final: 0.8252 (tpt) REVERT: H 154 ASP cc_start: 0.8084 (m-30) cc_final: 0.7730 (m-30) REVERT: I 143 ASN cc_start: 0.8424 (m-40) cc_final: 0.7199 (p0) REVERT: I 191 TYR cc_start: 0.8067 (t80) cc_final: 0.7552 (t80) REVERT: J 218 ASP cc_start: 0.8097 (m-30) cc_final: 0.7273 (m-30) REVERT: K 143 ASN cc_start: 0.8199 (m-40) cc_final: 0.7158 (p0) REVERT: L 218 ASP cc_start: 0.8577 (m-30) cc_final: 0.7742 (m-30) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.3894 time to fit residues: 110.1744 Evaluate side-chains 134 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 53 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21870 Z= 0.182 Angle : 0.632 11.334 29700 Z= 0.315 Chirality : 0.048 0.295 3486 Planarity : 0.004 0.047 3753 Dihedral : 8.297 62.198 3960 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.04 % Allowed : 1.16 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.73 (0.16), residues: 2649 helix: 1.23 (0.25), residues: 396 sheet: -0.30 (0.17), residues: 861 loop : -1.09 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 222 HIS 0.004 0.001 HIS B 142 PHE 0.021 0.002 PHE L 176 TYR 0.016 0.002 TYR A 233 ARG 0.007 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.670 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: C 168 MET cc_start: 0.7970 (tpp) cc_final: 0.7507 (tpp) REVERT: G 143 ASN cc_start: 0.8415 (m-40) cc_final: 0.7408 (p0) REVERT: G 191 TYR cc_start: 0.8468 (t80) cc_final: 0.8228 (t80) REVERT: H 121 MET cc_start: 0.8537 (tpt) cc_final: 0.8210 (tpt) REVERT: H 154 ASP cc_start: 0.8004 (m-30) cc_final: 0.7730 (m-30) REVERT: I 191 TYR cc_start: 0.7944 (t80) cc_final: 0.7366 (t80) REVERT: J 10 GLU cc_start: 0.8019 (tp30) cc_final: 0.7804 (tm-30) REVERT: J 121 MET cc_start: 0.8577 (tpt) cc_final: 0.8327 (tpt) REVERT: J 218 ASP cc_start: 0.7952 (m-30) cc_final: 0.7127 (m-30) REVERT: L 121 MET cc_start: 0.8396 (tpp) cc_final: 0.8194 (tpt) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.3579 time to fit residues: 112.2395 Evaluate side-chains 143 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN G 6 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21870 Z= 0.273 Angle : 0.663 11.357 29700 Z= 0.331 Chirality : 0.048 0.290 3486 Planarity : 0.005 0.059 3753 Dihedral : 8.145 58.185 3960 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.80 (0.16), residues: 2649 helix: 1.18 (0.26), residues: 396 sheet: -0.29 (0.17), residues: 855 loop : -1.19 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 222 HIS 0.006 0.001 HIS D 26 PHE 0.025 0.002 PHE L 176 TYR 0.025 0.002 TYR K 191 ARG 0.010 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 2.420 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: D 123 ARG cc_start: 0.7848 (pmt-80) cc_final: 0.7525 (ttp80) REVERT: G 143 ASN cc_start: 0.8487 (m-40) cc_final: 0.7436 (p0) REVERT: G 159 LEU cc_start: 0.7424 (tp) cc_final: 0.7214 (tp) REVERT: H 121 MET cc_start: 0.8505 (tpt) cc_final: 0.8200 (tpt) REVERT: H 154 ASP cc_start: 0.7953 (m-30) cc_final: 0.7689 (m-30) REVERT: I 191 TYR cc_start: 0.8108 (t80) cc_final: 0.7538 (t80) REVERT: K 195 LYS cc_start: 0.8649 (mppt) cc_final: 0.8191 (mmmt) REVERT: L 154 ASP cc_start: 0.7788 (m-30) cc_final: 0.7546 (m-30) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.3635 time to fit residues: 111.4322 Evaluate side-chains 137 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 0.0000 chunk 142 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 155 optimal weight: 0.0570 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21870 Z= 0.169 Angle : 0.628 12.049 29700 Z= 0.313 Chirality : 0.048 0.338 3486 Planarity : 0.005 0.078 3753 Dihedral : 7.698 55.688 3960 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.60 (0.16), residues: 2649 helix: 1.30 (0.25), residues: 396 sheet: -0.11 (0.18), residues: 828 loop : -1.06 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 222 HIS 0.004 0.001 HIS D 26 PHE 0.022 0.002 PHE L 176 TYR 0.021 0.001 TYR F 83 ARG 0.013 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.872 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: C 168 MET cc_start: 0.7992 (tpp) cc_final: 0.7576 (tpp) REVERT: D 123 ARG cc_start: 0.7821 (pmt-80) cc_final: 0.7566 (ttp80) REVERT: G 143 ASN cc_start: 0.8411 (m-40) cc_final: 0.7351 (p0) REVERT: H 10 GLU cc_start: 0.8184 (tp30) cc_final: 0.7797 (tm-30) REVERT: H 121 MET cc_start: 0.8506 (tpt) cc_final: 0.8182 (tpt) REVERT: I 191 TYR cc_start: 0.8042 (t80) cc_final: 0.7400 (t80) REVERT: J 121 MET cc_start: 0.8458 (tpt) cc_final: 0.8106 (tpt) REVERT: K 195 LYS cc_start: 0.8559 (mppt) cc_final: 0.8187 (mmmt) REVERT: L 121 MET cc_start: 0.8320 (tpp) cc_final: 0.8071 (tpt) REVERT: L 154 ASP cc_start: 0.7987 (m-30) cc_final: 0.7753 (m-30) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3601 time to fit residues: 112.8093 Evaluate side-chains 145 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 161 optimal weight: 0.0050 chunk 128 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 36 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21870 Z= 0.208 Angle : 0.631 12.175 29700 Z= 0.315 Chirality : 0.047 0.306 3486 Planarity : 0.005 0.094 3753 Dihedral : 7.565 56.576 3960 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.57 (0.16), residues: 2649 helix: 1.24 (0.25), residues: 396 sheet: -0.18 (0.18), residues: 861 loop : -0.97 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 153 HIS 0.007 0.001 HIS G 36 PHE 0.022 0.002 PHE L 176 TYR 0.027 0.002 TYR K 191 ARG 0.009 0.001 ARG I 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.422 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: symmetry clash REVERT: C 168 MET cc_start: 0.8033 (tpp) cc_final: 0.7595 (tpp) REVERT: D 123 ARG cc_start: 0.7801 (pmt-80) cc_final: 0.7447 (ttp80) REVERT: G 143 ASN cc_start: 0.8357 (m-40) cc_final: 0.7428 (p0) REVERT: H 10 GLU cc_start: 0.8176 (tp30) cc_final: 0.7769 (tm-30) REVERT: H 121 MET cc_start: 0.8582 (tpt) cc_final: 0.8239 (tpt) REVERT: I 191 TYR cc_start: 0.8154 (t80) cc_final: 0.7494 (t80) REVERT: J 121 MET cc_start: 0.8375 (tpt) cc_final: 0.8110 (tpp) REVERT: K 195 LYS cc_start: 0.8609 (mppt) cc_final: 0.8250 (mmmt) REVERT: L 121 MET cc_start: 0.8322 (tpp) cc_final: 0.8086 (tpt) REVERT: L 154 ASP cc_start: 0.7700 (m-30) cc_final: 0.7491 (m-30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3623 time to fit residues: 112.8472 Evaluate side-chains 147 residues out of total 2325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** I 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** 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 = 0.3280 r_free = 0.3280 target = 0.046402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036143 restraints weight = 189662.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037085 restraints weight = 112436.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.037727 restraints weight = 78968.855| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21870 Z= 0.233 Angle : 0.647 12.143 29700 Z= 0.325 Chirality : 0.047 0.297 3486 Planarity : 0.005 0.098 3753 Dihedral : 7.501 56.716 3960 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.70 (0.16), residues: 2649 helix: 1.13 (0.25), residues: 399 sheet: -0.29 (0.18), residues: 840 loop : -1.02 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 153 HIS 0.004 0.001 HIS B 159 PHE 0.021 0.002 PHE L 176 TYR 0.023 0.002 TYR B 83 ARG 0.016 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.81 seconds wall clock time: 76 minutes 3.38 seconds (4563.38 seconds total)