Starting phenix.real_space_refine on Wed Feb 21 14:11:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mki_23895/02_2024/7mki_23895_updated.pdb" } resolution = 3.5 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= 0.008 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 95 5.49 5 Mg 1 5.21 5 S 128 5.16 5 C 19111 2.51 5 N 5460 2.21 5 O 6122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 7": "OE1" <-> "OE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "G GLU 229": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 229": "OE1" <-> "OE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 218": "OE1" <-> "OE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I ASP 254": "OD1" <-> "OD2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I ARG 371": "NH1" <-> "NH2" Residue "I PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 396": "OD1" <-> "OD2" Residue "I PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "I PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 516": "OD1" <-> "OD2" Residue "I ASP 549": "OD1" <-> "OD2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I ASP 826": "OD1" <-> "OD2" Residue "I ASP 842": "OD1" <-> "OD2" Residue "I GLU 848": "OE1" <-> "OE2" Residue "I GLU 859": "OE1" <-> "OE2" Residue "I GLU 867": "OE1" <-> "OE2" Residue "I GLU 876": "OE1" <-> "OE2" Residue "I GLU 898": "OE1" <-> "OE2" Residue "I GLU 899": "OE1" <-> "OE2" Residue "I ASP 1040": "OD1" <-> "OD2" Residue "I TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1088": "OD1" <-> "OD2" Residue "I ASP 1126": "OD1" <-> "OD2" Residue "I ARG 1147": "NH1" <-> "NH2" Residue "I ASP 1154": "OD1" <-> "OD2" Residue "I GLU 1167": "OE1" <-> "OE2" Residue "I TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1296": "OD1" <-> "OD2" Residue "I ASP 1297": "OD1" <-> "OD2" Residue "I TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ASP 177": "OD1" <-> "OD2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J GLU 195": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 656": "OE1" <-> "OE2" Residue "J GLU 660": "OE1" <-> "OE2" Residue "J TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 812": "OD1" <-> "OD2" Residue "J ASP 889": "OD1" <-> "OD2" Residue "J ASP 1208": "OD1" <-> "OD2" Residue "J ASP 1273": "OD1" <-> "OD2" Residue "J GLU 1291": "OE1" <-> "OE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "L PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 349": "OE1" <-> "OE2" Residue "L GLU 381": "OE1" <-> "OE2" Residue "L TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 482": "OE1" <-> "OE2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L GLU 524": "OE1" <-> "OE2" Residue "L GLU 538": "OE1" <-> "OE2" Residue "L ASP 546": "OD1" <-> "OD2" Residue "L TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 605": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30919 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 998 Classifications: {'DNA': 49} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1808 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1714 Classifications: {'peptide': 223} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "J" Number of atoms: 10377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10377 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1278} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3787 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 450} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 957 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15536 SG CYS J 70 100.607 129.805 113.399 1.00 58.80 S ATOM 15550 SG CYS J 72 98.437 132.572 114.843 1.00 60.73 S ATOM 15658 SG CYS J 85 101.740 131.565 116.494 1.00 77.39 S ATOM 15682 SG CYS J 88 98.685 129.106 116.392 1.00 70.87 S ATOM 21365 SG CYS J 814 125.243 72.789 87.626 1.00 53.88 S ATOM 21930 SG CYS J 888 121.798 74.142 88.527 1.00 45.02 S ATOM 21981 SG CYS J 895 123.405 75.043 85.177 1.00 34.28 S ATOM 22002 SG CYS J 898 122.218 71.628 85.656 1.00 39.66 S Time building chain proxies: 15.94, per 1000 atoms: 0.52 Number of scatterers: 30919 At special positions: 0 Unit cell: (151.41, 182.31, 186.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 128 16.00 P 95 15.00 Mg 1 11.99 O 6122 8.00 N 5460 7.00 C 19111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 12 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 35 sheets defined 35.1% alpha, 8.5% beta 39 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 14.89 Creating SS restraints... Processing helix chain 'G' and resid 36 through 49 removed outlier: 3.700A pdb=" N ALA G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 87 removed outlier: 4.017A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 230 removed outlier: 3.822A pdb=" N GLU G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 226 Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.660A pdb=" N SER I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 347 through 353 Processing helix chain 'I' and resid 359 through 370 removed outlier: 3.983A pdb=" N MET I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 378 through 388 removed outlier: 3.787A pdb=" N GLU I 382 " --> pdb=" O ARG I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 479 Processing helix chain 'I' and resid 496 through 507 removed outlier: 3.701A pdb=" N ALA I 501 " --> pdb=" O PRO I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 526 Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 4.225A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 738 through 740 No H-bonds generated for 'chain 'I' and resid 738 through 740' Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 978 Processing helix chain 'I' and resid 996 through 999 removed outlier: 3.836A pdb=" N GLU I 999 " --> pdb=" O ARG I 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 996 through 999' Processing helix chain 'I' and resid 1008 through 1037 removed outlier: 4.613A pdb=" N GLU I1012 " --> pdb=" O GLN I1008 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN I1013 " --> pdb=" O ASN I1009 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) Processing helix chain 'I' and resid 1101 through 1104 No H-bonds generated for 'chain 'I' and resid 1101 through 1104' Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1139 through 1148 Processing helix chain 'I' and resid 1168 through 1175 removed outlier: 3.569A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1242 No H-bonds generated for 'chain 'I' and resid 1239 through 1242' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 4.333A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1322 through 1331 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 115 through 118 No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 123 through 128 removed outlier: 3.632A pdb=" N LEU J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 139 removed outlier: 4.068A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.551A pdb=" N GLU J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 Processing helix chain 'J' and resid 234 through 237 removed outlier: 3.883A pdb=" N MET J 237 " --> pdb=" O PRO J 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 234 through 237' Processing helix chain 'J' and resid 265 through 285 Processing helix chain 'J' and resid 289 through 305 removed outlier: 5.569A pdb=" N VAL J 303 " --> pdb=" O MET J 298 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP J 304 " --> pdb=" O LEU J 299 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA J 305 " --> pdb=" O GLN J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 388 Processing helix chain 'J' and resid 394 through 402 Processing helix chain 'J' and resid 408 through 416 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 451 through 457 removed outlier: 4.223A pdb=" N ALA J 455 " --> pdb=" O LEU J 452 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR J 457 " --> pdb=" O CYS J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 538 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.887A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 611 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 641 through 643 No H-bonds generated for 'chain 'J' and resid 641 through 643' Processing helix chain 'J' and resid 650 through 668 Processing helix chain 'J' and resid 675 through 701 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 769 through 803 removed outlier: 3.785A pdb=" N THR J 776 " --> pdb=" O TYR J 772 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU J 788 " --> pdb=" O ALA J 784 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 839 Processing helix chain 'J' and resid 866 through 875 removed outlier: 3.720A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 916 through 928 Proline residue: J 926 - end of helix Processing helix chain 'J' and resid 1069 through 1071 No H-bonds generated for 'chain 'J' and resid 1069 through 1071' Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.997A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 Processing helix chain 'J' and resid 1282 through 1293 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1320 through 1323 No H-bonds generated for 'chain 'J' and resid 1320 through 1323' Processing helix chain 'J' and resid 1328 through 1337 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1363 through 1372 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 56 Processing helix chain 'K' and resid 61 through 79 removed outlier: 3.901A pdb=" N GLU K 79 " --> pdb=" O GLN K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 113 through 136 removed outlier: 3.777A pdb=" N ILE L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU L 136 " --> pdb=" O CYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'L' and resid 158 through 161 No H-bonds generated for 'chain 'L' and resid 158 through 161' Processing helix chain 'L' and resid 215 through 234 Processing helix chain 'L' and resid 246 through 258 Processing helix chain 'L' and resid 263 through 289 Processing helix chain 'L' and resid 299 through 306 removed outlier: 3.682A pdb=" N LEU L 305 " --> pdb=" O ASN L 301 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 317 No H-bonds generated for 'chain 'L' and resid 314 through 317' Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 330 through 332 No H-bonds generated for 'chain 'L' and resid 330 through 332' Processing helix chain 'L' and resid 334 through 351 removed outlier: 3.845A pdb=" N GLN L 342 " --> pdb=" O HIS L 338 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS L 343 " --> pdb=" O ARG L 339 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR L 351 " --> pdb=" O ILE L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 391 removed outlier: 5.383A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 387 " --> pdb=" O ASN L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 417 Processing helix chain 'L' and resid 421 through 423 No H-bonds generated for 'chain 'L' and resid 421 through 423' Processing helix chain 'L' and resid 427 through 446 Processing helix chain 'L' and resid 454 through 474 removed outlier: 3.607A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 486 Processing helix chain 'L' and resid 493 through 500 Processing helix chain 'L' and resid 519 through 521 No H-bonds generated for 'chain 'L' and resid 519 through 521' Processing helix chain 'L' and resid 531 through 550 removed outlier: 3.519A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 562 Processing helix chain 'L' and resid 573 through 579 Processing helix chain 'L' and resid 584 through 598 Processing helix chain 'L' and resid 604 through 610 removed outlier: 4.238A pdb=" N PHE L 610 " --> pdb=" O VAL L 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 23 through 28 Processing sheet with id= B, first strand: chain 'G' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'G' and resid 97 through 99 Processing sheet with id= D, first strand: chain 'G' and resid 102 through 105 Processing sheet with id= E, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.702A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 13 through 17 removed outlier: 3.518A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= H, first strand: chain 'H' and resid 53 through 61 removed outlier: 6.970A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'I' and resid 116 through 123 removed outlier: 4.627A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= L, first strand: chain 'I' and resid 154 through 159 Processing sheet with id= M, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= O, first strand: chain 'I' and resid 588 through 592 Processing sheet with id= P, first strand: chain 'I' and resid 633 through 635 Processing sheet with id= Q, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.105A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.374A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 830 through 833 removed outlier: 3.713A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 887 through 889 Processing sheet with id= U, first strand: chain 'I' and resid 755 through 758 removed outlier: 6.171A pdb=" N ILE I 765 " --> pdb=" O TYR I 756 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.407A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 836 through 841 Processing sheet with id= X, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.642A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 252 through 254 removed outlier: 3.697A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AA, first strand: chain 'J' and resid 548 through 550 Processing sheet with id= AB, first strand: chain 'J' and resid 553 through 556 Processing sheet with id= AC, first strand: chain 'J' and resid 820 through 822 Processing sheet with id= AD, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.718A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AF, first strand: chain 'J' and resid 1034 through 1036 removed outlier: 3.860A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.578A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL J1107 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 1162 through 1164 Processing sheet with id= AI, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.630A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 12.61 Time building geometry restraints manager: 12.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6918 1.33 - 1.45: 6697 1.45 - 1.58: 17533 1.58 - 1.70: 196 1.70 - 1.82: 234 Bond restraints: 31578 Sorted by residual: bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.824 -0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.821 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C3 1N7 J1504 " pdb=" C4 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.736 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.725 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 31573 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 1031 105.68 - 112.78: 17068 112.78 - 119.89: 10716 119.89 - 126.99: 13783 126.99 - 134.10: 457 Bond angle restraints: 43055 Sorted by residual: angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" C LEU I 484 " pdb=" N ASP I 485 " pdb=" CA ASP I 485 " ideal model delta sigma weight residual 121.70 130.63 -8.93 1.80e+00 3.09e-01 2.46e+01 angle pdb=" N ARG L 603 " pdb=" CA ARG L 603 " pdb=" C ARG L 603 " ideal model delta sigma weight residual 114.75 108.61 6.14 1.26e+00 6.30e-01 2.37e+01 angle pdb=" C GLN I 517 " pdb=" N ASN I 518 " pdb=" CA ASN I 518 " ideal model delta sigma weight residual 122.86 115.42 7.44 1.53e+00 4.27e-01 2.37e+01 angle pdb=" C LEU I 397 " pdb=" N SER I 398 " pdb=" CA SER I 398 " ideal model delta sigma weight residual 121.70 129.66 -7.96 1.80e+00 3.09e-01 1.96e+01 ... (remaining 43050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 18576 35.83 - 71.65: 777 71.65 - 107.48: 30 107.48 - 143.30: 0 143.30 - 179.13: 1 Dihedral angle restraints: 19384 sinusoidal: 8804 harmonic: 10580 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual 180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA ILE L 500 " pdb=" C ILE L 500 " pdb=" N ALA L 501 " pdb=" CA ALA L 501 " ideal model delta harmonic sigma weight residual 180.00 -149.17 -30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA VAL K 32 " pdb=" C VAL K 32 " pdb=" N GLY K 33 " pdb=" CA GLY K 33 " ideal model delta harmonic sigma weight residual 180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 19381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4603 0.092 - 0.184: 314 0.184 - 0.276: 8 0.276 - 0.368: 1 0.368 - 0.460: 3 Chirality restraints: 4929 Sorted by residual: chirality pdb=" C19 1N7 J1504 " pdb=" C18 1N7 J1504 " pdb=" C2 1N7 J1504 " pdb=" C3 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.53 -2.99 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.96 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.91 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4926 not shown) Planarity restraints: 5275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 898 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU I 898 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU I 898 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU I 899 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J1184 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO J1185 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO J1185 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO J1185 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 189 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO I 190 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 190 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 190 " -0.031 5.00e-02 4.00e+02 ... (remaining 5272 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1458 2.72 - 3.26: 29210 3.26 - 3.81: 47869 3.81 - 4.35: 59847 4.35 - 4.90: 102839 Nonbonded interactions: 241223 Sorted by model distance: nonbonded pdb=" OG1 THR I 131 " pdb=" O THR I 135 " model vdw 2.170 2.440 nonbonded pdb=" OH TYR I 367 " pdb=" OE2 GLU I 374 " model vdw 2.179 2.440 nonbonded pdb=" OE1 GLU I1222 " pdb=" OH TYR J 512 " model vdw 2.180 2.440 nonbonded pdb=" NH2 ARG I 528 " pdb=" O SER I 576 " model vdw 2.190 2.520 nonbonded pdb=" O SER J 775 " pdb=" OG SER J 775 " model vdw 2.195 2.440 ... (remaining 241218 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 'G' and (resid 5 through 158 or resid 167 through 233)) selection = (chain 'H' and resid 5 through 233) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.300 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: 5.550 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 92.930 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.008 0.292 31578 Z= 0.466 Angle : 0.761 11.808 43055 Z= 0.436 Chirality : 0.049 0.460 4929 Planarity : 0.005 0.066 5275 Dihedral : 17.011 179.128 12564 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.83 % Rotamer: Outliers : 5.35 % Allowed : 11.74 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -1.84 (0.13), residues: 3652 helix: -0.15 (0.14), residues: 1401 sheet: -1.40 (0.24), residues: 446 loop : -2.07 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 33 HIS 0.009 0.001 HIS J 777 PHE 0.021 0.002 PHE J 437 TYR 0.022 0.002 TYR G 177 ARG 0.004 0.001 ARG I1246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 273 time to evaluate : 3.218 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8693 (t) REVERT: G 107 ILE cc_start: 0.8959 (pt) cc_final: 0.8703 (mt) REVERT: H 127 GLN cc_start: 0.8448 (mp10) cc_final: 0.8098 (mp10) REVERT: H 191 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7793 (ptt90) REVERT: I 160 ASP cc_start: 0.7504 (t70) cc_final: 0.6900 (t0) REVERT: I 387 ASN cc_start: 0.8543 (t0) cc_final: 0.8268 (t0) REVERT: I 514 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: I 516 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8569 (m-30) REVERT: I 524 ILE cc_start: 0.8490 (tt) cc_final: 0.8276 (tt) REVERT: I 601 ASP cc_start: 0.8100 (m-30) cc_final: 0.7625 (t0) REVERT: I 609 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8562 (mt) REVERT: I 829 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9192 (p) REVERT: I 1203 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5472 (t70) REVERT: I 1212 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (mp) REVERT: J 129 ASP cc_start: 0.7497 (t70) cc_final: 0.7202 (t0) REVERT: J 431 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7350 (ttm170) REVERT: J 1227 HIS cc_start: 0.7983 (m-70) cc_final: 0.7759 (m-70) REVERT: L 137 TYR cc_start: 0.2005 (OUTLIER) cc_final: 0.1305 (t80) REVERT: L 139 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5681 (tt0) REVERT: L 381 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6707 (mt-10) REVERT: L 573 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6244 (pp) outliers start: 168 outliers final: 85 residues processed: 428 average time/residue: 0.3889 time to fit residues: 272.4103 Evaluate side-chains 336 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 240 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 662 SER Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1203 ASP Chi-restraints excluded: chain I residue 1212 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 765 GLU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 190 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN ** I 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 554 HIS J 200 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31578 Z= 0.248 Angle : 0.571 12.113 43055 Z= 0.301 Chirality : 0.042 0.192 4929 Planarity : 0.004 0.062 5275 Dihedral : 15.958 178.442 5448 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.26 % Allowed : 14.99 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -1.43 (0.14), residues: 3652 helix: 0.32 (0.14), residues: 1407 sheet: -1.31 (0.24), residues: 425 loop : -1.92 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 315 HIS 0.007 0.001 HIS J 777 PHE 0.016 0.001 PHE I 337 TYR 0.017 0.001 TYR G 177 ARG 0.005 0.000 ARG L 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 258 time to evaluate : 3.631 Fit side-chains REVERT: G 70 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8644 (t) REVERT: H 65 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7030 (mt) REVERT: H 127 GLN cc_start: 0.8487 (mp10) cc_final: 0.8180 (mp10) REVERT: H 182 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7617 (ttt90) REVERT: H 191 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7828 (ptt90) REVERT: H 198 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8411 (mm) REVERT: I 160 ASP cc_start: 0.7397 (t70) cc_final: 0.6794 (t0) REVERT: I 387 ASN cc_start: 0.8518 (t0) cc_final: 0.8240 (t0) REVERT: I 504 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7459 (tt0) REVERT: I 514 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: I 524 ILE cc_start: 0.8432 (tt) cc_final: 0.8228 (tt) REVERT: I 601 ASP cc_start: 0.8116 (m-30) cc_final: 0.7638 (t0) REVERT: I 694 ARG cc_start: 0.6976 (mtm180) cc_final: 0.6763 (mtp-110) REVERT: I 903 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.6138 (mtm110) REVERT: I 1304 MET cc_start: 0.7784 (tpp) cc_final: 0.7481 (tpp) REVERT: J 431 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.7292 (ttm170) REVERT: J 756 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7610 (mt-10) REVERT: J 925 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: J 1236 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7210 (mm-30) REVERT: L 100 MET cc_start: 0.8106 (mtt) cc_final: 0.7609 (mtt) REVERT: L 137 TYR cc_start: 0.2003 (OUTLIER) cc_final: 0.1357 (t80) REVERT: L 139 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5791 (tt0) REVERT: L 381 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6582 (mt-10) REVERT: L 573 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6056 (pp) outliers start: 134 outliers final: 86 residues processed: 383 average time/residue: 0.4363 time to fit residues: 271.7657 Evaluate side-chains 339 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 244 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 230 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 339 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 302 optimal weight: 0.9980 chunk 336 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** I 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** J1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31578 Z= 0.226 Angle : 0.540 10.840 43055 Z= 0.285 Chirality : 0.041 0.181 4929 Planarity : 0.004 0.061 5275 Dihedral : 15.560 178.705 5402 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.65 % Rotamer: Outliers : 4.52 % Allowed : 15.95 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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: -1.13 (0.14), residues: 3652 helix: 0.66 (0.14), residues: 1410 sheet: -1.17 (0.25), residues: 420 loop : -1.83 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 315 HIS 0.006 0.001 HIS J 777 PHE 0.012 0.001 PHE J 437 TYR 0.016 0.001 TYR G 177 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 262 time to evaluate : 3.358 Fit side-chains REVERT: H 65 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6992 (mt) REVERT: H 127 GLN cc_start: 0.8510 (mp10) cc_final: 0.8202 (mp10) REVERT: H 182 ARG cc_start: 0.8036 (ttt90) cc_final: 0.7750 (ttt90) REVERT: H 191 ARG cc_start: 0.8160 (ptm160) cc_final: 0.7813 (ptt90) REVERT: H 198 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8424 (mm) REVERT: I 160 ASP cc_start: 0.7363 (t70) cc_final: 0.6669 (t0) REVERT: I 387 ASN cc_start: 0.8517 (t0) cc_final: 0.8234 (t0) REVERT: I 465 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6219 (ttm110) REVERT: I 504 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7390 (tt0) REVERT: I 514 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7675 (m-80) REVERT: I 524 ILE cc_start: 0.8431 (tt) cc_final: 0.8206 (tt) REVERT: I 601 ASP cc_start: 0.8087 (m-30) cc_final: 0.7635 (t0) REVERT: I 903 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.6122 (mtm110) REVERT: I 1142 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8027 (ttm110) REVERT: J 235 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8454 (pt0) REVERT: J 756 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7677 (mt-10) REVERT: J 925 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: J 1236 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7181 (mm-30) REVERT: K 55 GLU cc_start: 0.6653 (tt0) cc_final: 0.6429 (tt0) REVERT: L 100 MET cc_start: 0.8197 (mtt) cc_final: 0.7770 (mtt) REVERT: L 137 TYR cc_start: 0.2090 (OUTLIER) cc_final: 0.1420 (t80) REVERT: L 139 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5832 (tt0) REVERT: L 381 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6606 (mt-10) outliers start: 142 outliers final: 93 residues processed: 394 average time/residue: 0.3991 time to fit residues: 257.1612 Evaluate side-chains 350 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 249 time to evaluate : 7.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 687 ARG Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 569 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 340 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 322 optimal weight: 4.9990 chunk 97 optimal weight: 0.0020 overall best weight: 1.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN J 200 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31578 Z= 0.217 Angle : 0.529 10.418 43055 Z= 0.278 Chirality : 0.041 0.147 4929 Planarity : 0.004 0.059 5275 Dihedral : 15.439 178.613 5381 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.65 % Allowed : 16.71 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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: -0.97 (0.14), residues: 3652 helix: 0.82 (0.14), residues: 1411 sheet: -1.05 (0.25), residues: 419 loop : -1.77 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 315 HIS 0.005 0.001 HIS J 777 PHE 0.012 0.001 PHE I 337 TYR 0.017 0.001 TYR G 177 ARG 0.003 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 254 time to evaluate : 3.224 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8723 (t) REVERT: H 31 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8078 (mt) REVERT: H 65 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6845 (mt) REVERT: H 127 GLN cc_start: 0.8505 (mp10) cc_final: 0.8195 (mp10) REVERT: H 182 ARG cc_start: 0.8046 (ttt90) cc_final: 0.7778 (ttt90) REVERT: H 191 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7794 (ptt90) REVERT: H 198 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (mm) REVERT: I 160 ASP cc_start: 0.7330 (t70) cc_final: 0.6630 (t0) REVERT: I 369 MET cc_start: 0.8179 (ptm) cc_final: 0.7902 (ptm) REVERT: I 387 ASN cc_start: 0.8519 (t0) cc_final: 0.8234 (t0) REVERT: I 465 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6226 (ttm110) REVERT: I 504 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 514 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: I 524 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (tt) REVERT: I 601 ASP cc_start: 0.8089 (m-30) cc_final: 0.7649 (t0) REVERT: I 800 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7886 (mtp) REVERT: I 903 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.6145 (mtm110) REVERT: J 235 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: J 431 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: J 442 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7852 (pt) REVERT: J 756 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7648 (mt-10) REVERT: J 1236 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7119 (mm-30) REVERT: K 55 GLU cc_start: 0.6600 (tt0) cc_final: 0.6366 (tt0) REVERT: K 80 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.1337 (tp) REVERT: L 100 MET cc_start: 0.8200 (mtt) cc_final: 0.7832 (mtt) REVERT: L 137 TYR cc_start: 0.2246 (OUTLIER) cc_final: 0.1492 (t80) REVERT: L 139 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5863 (tt0) REVERT: L 273 MET cc_start: 0.6898 (mtm) cc_final: 0.6599 (mtp) REVERT: L 573 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6069 (pp) outliers start: 146 outliers final: 98 residues processed: 389 average time/residue: 0.4142 time to fit residues: 260.9926 Evaluate side-chains 359 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 246 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 132 HIS J 200 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** J 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 31578 Z= 0.487 Angle : 0.675 12.430 43055 Z= 0.350 Chirality : 0.047 0.182 4929 Planarity : 0.005 0.062 5275 Dihedral : 15.843 176.925 5375 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer: Outliers : 5.70 % Allowed : 16.61 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -1.34 (0.14), residues: 3652 helix: 0.37 (0.14), residues: 1422 sheet: -1.13 (0.24), residues: 424 loop : -1.90 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 33 HIS 0.009 0.001 HIS J 777 PHE 0.019 0.002 PHE J 437 TYR 0.020 0.002 TYR J1186 ARG 0.005 0.000 ARG I 944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 246 time to evaluate : 3.169 Fit side-chains REVERT: G 70 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8692 (t) REVERT: G 79 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8442 (tp) REVERT: H 65 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6767 (mt) REVERT: H 80 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: H 127 GLN cc_start: 0.8567 (mp10) cc_final: 0.8268 (mp10) REVERT: H 191 ARG cc_start: 0.8164 (ptm160) cc_final: 0.7796 (ptt90) REVERT: I 160 ASP cc_start: 0.7460 (t70) cc_final: 0.6778 (t0) REVERT: I 189 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7258 (t0) REVERT: I 387 ASN cc_start: 0.8515 (t0) cc_final: 0.8187 (t0) REVERT: I 465 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6252 (ttm110) REVERT: I 504 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7914 (tm-30) REVERT: I 514 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: I 601 ASP cc_start: 0.8309 (m-30) cc_final: 0.7719 (t0) REVERT: I 651 ASP cc_start: 0.7694 (t70) cc_final: 0.6906 (t0) REVERT: I 912 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7641 (p0) REVERT: I 1041 ASP cc_start: 0.8374 (t0) cc_final: 0.7656 (p0) REVERT: J 53 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7457 (ttm-80) REVERT: J 235 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: J 418 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7443 (mm-30) REVERT: J 431 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.6967 (ttm170) REVERT: J 604 MET cc_start: 0.8294 (ttm) cc_final: 0.8003 (ttm) REVERT: J 756 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7613 (mt-10) REVERT: K 55 GLU cc_start: 0.6576 (tt0) cc_final: 0.6373 (tt0) REVERT: L 100 MET cc_start: 0.8226 (mtt) cc_final: 0.7977 (mtt) REVERT: L 137 TYR cc_start: 0.2242 (OUTLIER) cc_final: 0.1516 (t80) REVERT: L 139 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: L 573 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6137 (pp) outliers start: 179 outliers final: 125 residues processed: 413 average time/residue: 0.3951 time to fit residues: 266.5903 Evaluate side-chains 382 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 243 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 525 THR Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 565 GLU Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 596 ASP Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 660 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 912 ASP Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 592 VAL Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 767 LEU Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 811 GLU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 558 VAL Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 573 LEU Chi-restraints excluded: chain L residue 587 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 189 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 103 ASN G 127 GLN ** I 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31578 Z= 0.153 Angle : 0.502 8.781 43055 Z= 0.265 Chirality : 0.040 0.147 4929 Planarity : 0.004 0.056 5275 Dihedral : 15.311 178.195 5372 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.63 % Allowed : 19.03 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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 (0.14), residues: 3652 helix: 0.99 (0.14), residues: 1400 sheet: -0.96 (0.24), residues: 426 loop : -1.69 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 807 HIS 0.003 0.001 HIS J 777 PHE 0.009 0.001 PHE I 385 TYR 0.015 0.001 TYR G 177 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 266 time to evaluate : 4.002 Fit side-chains revert: symmetry clash REVERT: G 70 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8780 (t) REVERT: H 65 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6724 (mt) REVERT: H 80 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: H 127 GLN cc_start: 0.8464 (mp10) cc_final: 0.8121 (mp10) REVERT: H 182 ARG cc_start: 0.8050 (ttt90) cc_final: 0.7757 (ttt90) REVERT: H 191 ARG cc_start: 0.8025 (ptm160) cc_final: 0.7637 (ptt90) REVERT: I 30 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6823 (pt) REVERT: I 160 ASP cc_start: 0.7297 (t70) cc_final: 0.6541 (t0) REVERT: I 189 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7213 (t0) REVERT: I 369 MET cc_start: 0.8085 (ptm) cc_final: 0.7742 (ptm) REVERT: I 387 ASN cc_start: 0.8485 (t0) cc_final: 0.8227 (t0) REVERT: I 514 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: I 573 ASN cc_start: 0.7183 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: I 601 ASP cc_start: 0.8164 (m-30) cc_final: 0.7647 (t0) REVERT: I 955 GLN cc_start: 0.7316 (tp40) cc_final: 0.7036 (tp40) REVERT: I 1085 MET cc_start: 0.8971 (mmm) cc_final: 0.8770 (mmp) REVERT: I 1098 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8089 (mp) REVERT: I 1154 ASP cc_start: 0.7278 (t0) cc_final: 0.7059 (t0) REVERT: J 154 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5672 (mt) REVERT: J 235 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: J 442 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8026 (pt) REVERT: J 590 SER cc_start: 0.8897 (m) cc_final: 0.8554 (p) REVERT: J 604 MET cc_start: 0.8320 (ttm) cc_final: 0.8069 (ttm) REVERT: J 756 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7570 (mt-10) REVERT: J 1236 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7083 (mm-30) REVERT: J 1284 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7247 (mpt180) REVERT: J 1293 GLU cc_start: 0.5927 (mm-30) cc_final: 0.5618 (mm-30) REVERT: K 80 LEU cc_start: 0.3059 (OUTLIER) cc_final: 0.1495 (tp) REVERT: L 100 MET cc_start: 0.8160 (mtt) cc_final: 0.7853 (mtt) REVERT: L 137 TYR cc_start: 0.2089 (OUTLIER) cc_final: 0.1483 (t80) REVERT: L 139 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5848 (tt0) REVERT: L 273 MET cc_start: 0.6788 (mtm) cc_final: 0.6472 (mtp) REVERT: L 482 GLU cc_start: 0.6085 (tt0) cc_final: 0.5784 (mt-10) REVERT: L 573 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6034 (pp) outliers start: 114 outliers final: 72 residues processed: 373 average time/residue: 0.4265 time to fit residues: 260.7069 Evaluate side-chains 336 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 248 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 622 ASN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1098 LEU Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 759 ILE Chi-restraints excluded: chain J residue 800 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1284 ARG Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 263 optimal weight: 0.0050 chunk 204 optimal weight: 0.5980 chunk 303 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 359 optimal weight: 3.9990 chunk 224 optimal weight: 0.0980 chunk 219 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN J 294 ASN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31578 Z= 0.135 Angle : 0.483 7.984 43055 Z= 0.255 Chirality : 0.039 0.147 4929 Planarity : 0.004 0.053 5275 Dihedral : 15.131 178.531 5365 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.28 % Allowed : 19.22 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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: -0.55 (0.14), residues: 3652 helix: 1.23 (0.15), residues: 1410 sheet: -0.79 (0.24), residues: 434 loop : -1.59 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 807 HIS 0.004 0.000 HIS J 80 PHE 0.012 0.001 PHE I 906 TYR 0.013 0.001 TYR G 177 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 280 time to evaluate : 3.368 Fit side-chains revert: symmetry clash REVERT: G 226 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: H 65 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6555 (mt) REVERT: H 80 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6325 (mt-10) REVERT: H 127 GLN cc_start: 0.8428 (mp10) cc_final: 0.8084 (mp10) REVERT: H 182 ARG cc_start: 0.8073 (ttt90) cc_final: 0.7836 (ttt90) REVERT: H 191 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7578 (ptt90) REVERT: I 160 ASP cc_start: 0.7235 (t70) cc_final: 0.6512 (t0) REVERT: I 189 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7233 (t0) REVERT: I 369 MET cc_start: 0.8096 (ptm) cc_final: 0.7712 (ptm) REVERT: I 387 ASN cc_start: 0.8506 (t0) cc_final: 0.8183 (t0) REVERT: I 465 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6069 (ttm110) REVERT: I 504 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7474 (tt0) REVERT: I 514 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: I 573 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7022 (m-40) REVERT: I 601 ASP cc_start: 0.8113 (m-30) cc_final: 0.7655 (t0) REVERT: I 942 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6970 (p0) REVERT: I 955 GLN cc_start: 0.7360 (tp40) cc_final: 0.7097 (tp40) REVERT: I 1154 ASP cc_start: 0.7297 (t0) cc_final: 0.7088 (t0) REVERT: J 154 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5631 (mt) REVERT: J 235 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: J 442 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8124 (pt) REVERT: J 756 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7629 (mt-10) REVERT: K 80 LEU cc_start: 0.2973 (OUTLIER) cc_final: 0.1476 (tp) REVERT: L 129 GLN cc_start: 0.7165 (tp40) cc_final: 0.6943 (tp40) REVERT: L 137 TYR cc_start: 0.1743 (OUTLIER) cc_final: 0.1382 (t80) REVERT: L 139 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5823 (tt0) REVERT: L 277 MET cc_start: 0.5306 (tpt) cc_final: 0.5051 (tpp) REVERT: L 482 GLU cc_start: 0.6059 (tt0) cc_final: 0.5780 (mt-10) REVERT: L 514 ASP cc_start: 0.1672 (p0) cc_final: 0.1450 (p0) REVERT: L 573 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6103 (pp) outliers start: 103 outliers final: 65 residues processed: 373 average time/residue: 0.4490 time to fit residues: 279.4385 Evaluate side-chains 334 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 254 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 282 optimal weight: 30.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN J 200 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 338 HIS ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31578 Z= 0.218 Angle : 0.520 8.421 43055 Z= 0.272 Chirality : 0.041 0.149 4929 Planarity : 0.004 0.055 5275 Dihedral : 15.199 177.800 5349 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.41 % Allowed : 19.19 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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: -0.51 (0.14), residues: 3652 helix: 1.22 (0.14), residues: 1412 sheet: -0.73 (0.24), residues: 432 loop : -1.55 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 315 HIS 0.004 0.001 HIS J 777 PHE 0.018 0.001 PHE I 337 TYR 0.017 0.001 TYR G 177 ARG 0.003 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 257 time to evaluate : 3.213 Fit side-chains revert: symmetry clash REVERT: G 226 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: H 65 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6374 (mt) REVERT: H 80 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: H 107 ILE cc_start: 0.7050 (tp) cc_final: 0.6781 (mm) REVERT: H 127 GLN cc_start: 0.8472 (mp10) cc_final: 0.8130 (mp10) REVERT: H 182 ARG cc_start: 0.8068 (ttt90) cc_final: 0.7794 (ttt90) REVERT: H 191 ARG cc_start: 0.7971 (ptm160) cc_final: 0.7596 (ptt90) REVERT: I 160 ASP cc_start: 0.7263 (t70) cc_final: 0.6566 (t0) REVERT: I 189 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7257 (t0) REVERT: I 387 ASN cc_start: 0.8514 (t0) cc_final: 0.8150 (t0) REVERT: I 465 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6115 (ttp-110) REVERT: I 504 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7611 (tt0) REVERT: I 514 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: I 601 ASP cc_start: 0.8118 (m-30) cc_final: 0.7642 (t0) REVERT: I 942 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6970 (p0) REVERT: I 1154 ASP cc_start: 0.7254 (t0) cc_final: 0.7029 (t0) REVERT: J 53 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7355 (ptm160) REVERT: J 154 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5595 (mt) REVERT: J 235 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: J 431 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.6952 (ttm170) REVERT: J 442 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7947 (pt) REVERT: J 756 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7636 (mt-10) REVERT: J 1236 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7157 (mm-30) REVERT: K 55 GLU cc_start: 0.6044 (tt0) cc_final: 0.5834 (tt0) REVERT: K 80 LEU cc_start: 0.2925 (OUTLIER) cc_final: 0.1526 (tp) REVERT: L 137 TYR cc_start: 0.2010 (OUTLIER) cc_final: 0.1438 (t80) REVERT: L 139 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5864 (tt0) REVERT: L 277 MET cc_start: 0.5349 (tpt) cc_final: 0.5079 (tpp) REVERT: L 573 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6140 (pp) outliers start: 107 outliers final: 76 residues processed: 353 average time/residue: 0.4257 time to fit residues: 243.2063 Evaluate side-chains 347 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 255 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 573 ASN Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 ARG Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 314 optimal weight: 0.9990 chunk 335 optimal weight: 10.0000 chunk 201 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 316 optimal weight: 0.7980 chunk 333 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN H 66 HIS ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31578 Z= 0.159 Angle : 0.492 7.601 43055 Z= 0.258 Chirality : 0.040 0.148 4929 Planarity : 0.004 0.053 5275 Dihedral : 15.115 177.480 5349 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.09 % Allowed : 19.70 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % Twisted Proline : 0.70 % 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: -0.41 (0.14), residues: 3652 helix: 1.31 (0.14), residues: 1415 sheet: -0.71 (0.24), residues: 444 loop : -1.51 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J1193 HIS 0.004 0.001 HIS J 80 PHE 0.009 0.001 PHE I 337 TYR 0.015 0.001 TYR G 177 ARG 0.004 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 259 time to evaluate : 3.662 Fit side-chains revert: symmetry clash REVERT: G 226 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: H 65 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6478 (mt) REVERT: H 80 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: H 127 GLN cc_start: 0.8455 (mp10) cc_final: 0.8108 (mp10) REVERT: H 182 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7801 (ttt90) REVERT: H 191 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7626 (ptt90) REVERT: I 160 ASP cc_start: 0.7226 (t70) cc_final: 0.6495 (t0) REVERT: I 189 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7252 (t0) REVERT: I 369 MET cc_start: 0.7957 (ptm) cc_final: 0.7645 (ptm) REVERT: I 387 ASN cc_start: 0.8512 (t0) cc_final: 0.8124 (t0) REVERT: I 465 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6076 (ttm110) REVERT: I 504 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7471 (tt0) REVERT: I 514 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: I 601 ASP cc_start: 0.8108 (m-30) cc_final: 0.7646 (t0) REVERT: I 942 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6993 (p0) REVERT: J 154 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5579 (mt) REVERT: J 235 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8293 (pt0) REVERT: J 442 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7963 (pt) REVERT: J 756 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7593 (mt-10) REVERT: J 1236 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7062 (mm-30) REVERT: K 80 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.1664 (tp) REVERT: L 137 TYR cc_start: 0.1981 (OUTLIER) cc_final: 0.1401 (t80) REVERT: L 139 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5935 (tt0) REVERT: L 277 MET cc_start: 0.5392 (tpt) cc_final: 0.5133 (tpp) REVERT: L 514 ASP cc_start: 0.1870 (p0) cc_final: 0.1646 (p0) REVERT: L 573 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6116 (pp) outliers start: 97 outliers final: 77 residues processed: 346 average time/residue: 0.4210 time to fit residues: 236.7866 Evaluate side-chains 344 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 253 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 365 MET Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.7980 chunk 354 optimal weight: 0.0030 chunk 216 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 228 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN G 132 HIS I 139 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31578 Z= 0.161 Angle : 0.488 8.015 43055 Z= 0.256 Chirality : 0.040 0.147 4929 Planarity : 0.004 0.053 5275 Dihedral : 15.062 177.597 5349 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.93 % Allowed : 19.89 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % 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: -0.31 (0.14), residues: 3652 helix: 1.39 (0.14), residues: 1416 sheet: -0.61 (0.24), residues: 441 loop : -1.45 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.005 0.001 HIS J 80 PHE 0.017 0.001 PHE I 337 TYR 0.015 0.001 TYR G 177 ARG 0.005 0.000 ARG K 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7304 Ramachandran restraints generated. 3652 Oldfield, 0 Emsley, 3652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 267 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 226 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: H 65 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6533 (mt) REVERT: H 80 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: H 107 ILE cc_start: 0.6966 (tp) cc_final: 0.6701 (mm) REVERT: H 127 GLN cc_start: 0.8449 (mp10) cc_final: 0.8101 (mp10) REVERT: H 182 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7771 (ttt90) REVERT: H 191 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7621 (ptt90) REVERT: I 160 ASP cc_start: 0.7217 (t70) cc_final: 0.6499 (t0) REVERT: I 189 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7248 (t0) REVERT: I 369 MET cc_start: 0.8000 (ptm) cc_final: 0.7701 (ptm) REVERT: I 387 ASN cc_start: 0.8521 (t0) cc_final: 0.8069 (t0) REVERT: I 465 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6083 (ttm110) REVERT: I 504 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7465 (tt0) REVERT: I 514 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: I 601 ASP cc_start: 0.8145 (m-30) cc_final: 0.7612 (t0) REVERT: I 909 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6572 (tptp) REVERT: I 942 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6993 (p0) REVERT: J 154 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5560 (mt) REVERT: J 235 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: J 442 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7993 (pt) REVERT: J 756 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7540 (mt-10) REVERT: J 1236 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7052 (mm-30) REVERT: K 80 LEU cc_start: 0.2884 (OUTLIER) cc_final: 0.1589 (tp) REVERT: L 137 TYR cc_start: 0.1857 (OUTLIER) cc_final: 0.1125 (t80) REVERT: L 277 MET cc_start: 0.5575 (tpt) cc_final: 0.5302 (tpp) REVERT: L 482 GLU cc_start: 0.6004 (tt0) cc_final: 0.5779 (mt-10) REVERT: L 514 ASP cc_start: 0.1758 (p0) cc_final: 0.1518 (p0) REVERT: L 573 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6144 (pp) outliers start: 92 outliers final: 76 residues processed: 351 average time/residue: 0.4162 time to fit residues: 238.5795 Evaluate side-chains 346 residues out of total 3147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 257 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 465 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 942 ASP Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1222 GLU Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 232 ASN Chi-restraints excluded: chain J residue 235 GLU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 442 ILE Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 596 LEU Chi-restraints excluded: chain J residue 644 MET Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 738 ARG Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 903 LEU Chi-restraints excluded: chain J residue 931 THR Chi-restraints excluded: chain J residue 975 ILE Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1037 PHE Chi-restraints excluded: chain J residue 1107 VAL Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1190 ILE Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1219 ASP Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 137 TYR Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 488 LEU Chi-restraints excluded: chain L residue 519 LEU Chi-restraints excluded: chain L residue 527 THR Chi-restraints excluded: chain L residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 6.9990 chunk 315 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 272 optimal weight: 0.0020 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 304 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134573 restraints weight = 35111.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133282 restraints weight = 121521.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133784 restraints weight = 53768.488| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31578 Z= 0.169 Angle : 0.492 7.694 43055 Z= 0.258 Chirality : 0.040 0.147 4929 Planarity : 0.004 0.052 5275 Dihedral : 15.033 177.310 5342 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.06 % Allowed : 20.05 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.17 % 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: -0.28 (0.14), residues: 3652 helix: 1.41 (0.14), residues: 1420 sheet: -0.55 (0.24), residues: 439 loop : -1.45 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J1193 HIS 0.005 0.001 HIS J 80 PHE 0.009 0.001 PHE J 437 TYR 0.015 0.001 TYR G 177 ARG 0.004 0.000 ARG K 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5991.84 seconds wall clock time: 109 minutes 44.74 seconds (6584.74 seconds total)