Starting phenix.real_space_refine on Sun Feb 25 13:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/02_2024/7add_11724_updated.pdb" } resolution = 4.3 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= 0.003 sd= 0.017 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 98 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 32023 2.51 5 N 9121 2.21 5 O 10117 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 108": "OE1" <-> "OE2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f GLU 351": "OE1" <-> "OE2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f GLU 375": "OE1" <-> "OE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "a GLU 125": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a GLU 351": "OE1" <-> "OE2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a GLU 375": "OE1" <-> "OE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b GLU 108": "OE1" <-> "OE2" Residue "b GLU 125": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b GLU 351": "OE1" <-> "OE2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b GLU 375": "OE1" <-> "OE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c GLU 351": "OE1" <-> "OE2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c GLU 375": "OE1" <-> "OE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d GLU 351": "OE1" <-> "OE2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d GLU 375": "OE1" <-> "OE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e GLU 108": "OE1" <-> "OE2" Residue "e GLU 125": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e GLU 351": "OE1" <-> "OE2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 181": "OE1" <-> "OE2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 219": "NH1" <-> "NH2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 29": "OE1" <-> "OE2" Residue "V ARG 33": "NH1" <-> "NH2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V GLU 136": "OE1" <-> "OE2" Residue "V GLU 165": "OE1" <-> "OE2" Residue "V GLU 204": "OE1" <-> "OE2" Residue "V GLU 261": "OE1" <-> "OE2" Residue "V ARG 265": "NH1" <-> "NH2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W GLU 74": "OE1" <-> "OE2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X GLU 244": "OE1" <-> "OE2" Residue "X ARG 268": "NH1" <-> "NH2" Residue "X GLU 308": "OE1" <-> "OE2" Residue "X ARG 371": "NH1" <-> "NH2" Residue "X ARG 451": "NH1" <-> "NH2" Residue "X GLU 546": "OE1" <-> "OE2" Residue "X GLU 565": "OE1" <-> "OE2" Residue "X ARG 647": "NH1" <-> "NH2" Residue "X GLU 705": "OE1" <-> "OE2" Residue "X GLU 825": "OE1" <-> "OE2" Residue "X ARG 903": "NH1" <-> "NH2" Residue "X GLU 940": "OE1" <-> "OE2" Residue "X GLU 950": "OE1" <-> "OE2" Residue "X GLU 963": "OE1" <-> "OE2" Residue "X ARG 996": "NH1" <-> "NH2" Residue "X GLU 1020": "OE1" <-> "OE2" Residue "X ARG 1034": "NH1" <-> "NH2" Residue "X ARG 1106": "NH1" <-> "NH2" Residue "X GLU 1137": "OE1" <-> "OE2" Residue "X ARG 1171": "NH1" <-> "NH2" Residue "X GLU 1174": "OE1" <-> "OE2" Residue "X GLU 1279": "OE1" <-> "OE2" Residue "X GLU 1321": "OE1" <-> "OE2" Residue "X GLU 1329": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y ARG 101": "NH1" <-> "NH2" Residue "Y ARG 133": "NH1" <-> "NH2" Residue "Y ARG 314": "NH1" <-> "NH2" Residue "Y GLU 375": "OE1" <-> "OE2" Residue "Y GLU 386": "OE1" <-> "OE2" Residue "Y GLU 414": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y ARG 515": "NH1" <-> "NH2" Residue "Y ARG 634": "NH1" <-> "NH2" Residue "Y ARG 692": "NH1" <-> "NH2" Residue "Y GLU 714": "OE1" <-> "OE2" Residue "Y GLU 827": "OE1" <-> "OE2" Residue "Y ARG 836": "NH1" <-> "NH2" Residue "Y GLU 866": "OE1" <-> "OE2" Residue "Y GLU 913": "OE1" <-> "OE2" Residue "Y ARG 933": "NH1" <-> "NH2" Residue "Y ARG 943": "NH1" <-> "NH2" Residue "Y ARG 1036": "NH1" <-> "NH2" Residue "Y GLU 1146": "OE1" <-> "OE2" Residue "Y ARG 1148": "NH1" <-> "NH2" Residue "Y GLU 1187": "OE1" <-> "OE2" Residue "Y GLU 1188": "OE1" <-> "OE2" Residue "Y GLU 1215": "OE1" <-> "OE2" Residue "Y GLU 1254": "OE1" <-> "OE2" Residue "Y ARG 1258": "NH1" <-> "NH2" Residue "Y GLU 1327": "OE1" <-> "OE2" Residue "Y ARG 1345": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51610 Number of models: 1 Model: "" Number of chains: 26 Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} Chain: "W" 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: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1283} Chain: "Y" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "L" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 704 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "R" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 22} Chain breaks: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 54.748 119.874 118.065 1.00187.89 S ATOM 39518 SG CYS Y 72 54.953 116.532 119.073 1.00178.12 S ATOM 39626 SG CYS Y 85 52.811 118.016 121.591 1.00190.63 S ATOM 45338 SG CYS Y 814 69.868 185.845 119.810 1.00113.47 S ATOM 45903 SG CYS Y 888 72.009 181.687 119.875 1.00100.48 S ATOM 45954 SG CYS Y 895 68.988 181.850 118.048 1.00102.60 S ATOM 45975 SG CYS Y 898 72.521 184.573 117.833 1.00 95.45 S Time building chain proxies: 24.26, per 1000 atoms: 0.47 Number of scatterers: 51610 At special positions: 0 Unit cell: (162.44, 228.16, 194.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 98 15.00 Mg 6 11.99 F 15 9.00 O 10117 8.00 N 9121 7.00 C 32023 6.00 Be 5 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.32 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " Number of angles added : 6 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 47 sheets defined 35.7% alpha, 11.9% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 22.57 Creating SS restraints... Processing helix chain 'f' and resid 4 through 7 No H-bonds generated for 'chain 'f' and resid 4 through 7' Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 31 through 44 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 126 through 128 No H-bonds generated for 'chain 'f' and resid 126 through 128' Processing helix chain 'f' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU f 162 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 198 Processing helix chain 'f' and resid 213 through 221 removed outlier: 3.916A pdb=" N ARG f 221 " --> pdb=" O THR f 217 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 255 Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 292 through 302 removed outlier: 4.274A pdb=" N ARG f 296 " --> pdb=" O ALA f 293 " (cutoff:3.500A) Proline residue: f 297 - end of helix Processing helix chain 'f' and resid 326 through 338 removed outlier: 4.683A pdb=" N GLY f 337 " --> pdb=" O GLU f 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR f 338 " --> pdb=" O GLU f 334 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 352 Processing helix chain 'f' and resid 368 through 371 Processing helix chain 'f' and resid 374 through 388 Processing helix chain 'f' and resid 393 through 404 Processing helix chain 'f' and resid 409 through 416 Processing helix chain 'a' and resid 4 through 7 No H-bonds generated for 'chain 'a' and resid 4 through 7' Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 31 through 44 Processing helix chain 'a' and resid 83 through 89 Processing helix chain 'a' and resid 126 through 128 No H-bonds generated for 'chain 'a' and resid 126 through 128' Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU a 162 " --> pdb=" O THR a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 198 Processing helix chain 'a' and resid 213 through 221 removed outlier: 3.915A pdb=" N ARG a 221 " --> pdb=" O THR a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 255 Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 292 through 302 removed outlier: 4.273A pdb=" N ARG a 296 " --> pdb=" O ALA a 293 " (cutoff:3.500A) Proline residue: a 297 - end of helix Processing helix chain 'a' and resid 326 through 338 removed outlier: 4.683A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR a 338 " --> pdb=" O GLU a 334 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 352 Processing helix chain 'a' and resid 368 through 371 Processing helix chain 'a' and resid 374 through 388 Processing helix chain 'a' and resid 393 through 404 Processing helix chain 'a' and resid 409 through 416 Processing helix chain 'b' and resid 4 through 7 No H-bonds generated for 'chain 'b' and resid 4 through 7' Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 126 through 128 No H-bonds generated for 'chain 'b' and resid 126 through 128' Processing helix chain 'b' and resid 156 through 165 removed outlier: 3.645A pdb=" N LEU b 162 " --> pdb=" O THR b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 198 Processing helix chain 'b' and resid 213 through 221 removed outlier: 3.916A pdb=" N ARG b 221 " --> pdb=" O THR b 217 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 255 Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 292 through 302 removed outlier: 4.274A pdb=" N ARG b 296 " --> pdb=" O ALA b 293 " (cutoff:3.500A) Proline residue: b 297 - end of helix Processing helix chain 'b' and resid 326 through 338 removed outlier: 4.683A pdb=" N GLY b 337 " --> pdb=" O GLU b 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR b 338 " --> pdb=" O GLU b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 352 Processing helix chain 'b' and resid 368 through 371 Processing helix chain 'b' and resid 374 through 388 Processing helix chain 'b' and resid 393 through 404 Processing helix chain 'b' and resid 409 through 416 Processing helix chain 'c' and resid 4 through 7 No H-bonds generated for 'chain 'c' and resid 4 through 7' Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 31 through 44 Processing helix chain 'c' and resid 83 through 89 Processing helix chain 'c' and resid 126 through 128 No H-bonds generated for 'chain 'c' and resid 126 through 128' Processing helix chain 'c' and resid 156 through 165 removed outlier: 3.645A pdb=" N LEU c 162 " --> pdb=" O THR c 158 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 198 Processing helix chain 'c' and resid 213 through 221 removed outlier: 3.915A pdb=" N ARG c 221 " --> pdb=" O THR c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 255 Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 292 through 302 removed outlier: 4.273A pdb=" N ARG c 296 " --> pdb=" O ALA c 293 " (cutoff:3.500A) Proline residue: c 297 - end of helix Processing helix chain 'c' and resid 326 through 338 removed outlier: 4.682A pdb=" N GLY c 337 " --> pdb=" O GLU c 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR c 338 " --> pdb=" O GLU c 334 " (cutoff:3.500A) Processing helix chain 'c' and resid 347 through 352 Processing helix chain 'c' and resid 368 through 371 Processing helix chain 'c' and resid 374 through 388 Processing helix chain 'c' and resid 393 through 404 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'd' and resid 4 through 7 No H-bonds generated for 'chain 'd' and resid 4 through 7' Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 31 through 44 Processing helix chain 'd' and resid 83 through 89 Processing helix chain 'd' and resid 126 through 128 No H-bonds generated for 'chain 'd' and resid 126 through 128' Processing helix chain 'd' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 198 Processing helix chain 'd' and resid 213 through 221 removed outlier: 3.915A pdb=" N ARG d 221 " --> pdb=" O THR d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 255 Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 292 through 302 removed outlier: 4.273A pdb=" N ARG d 296 " --> pdb=" O ALA d 293 " (cutoff:3.500A) Proline residue: d 297 - end of helix Processing helix chain 'd' and resid 326 through 338 removed outlier: 4.683A pdb=" N GLY d 337 " --> pdb=" O GLU d 333 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR d 338 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 347 through 352 Processing helix chain 'd' and resid 368 through 371 Processing helix chain 'd' and resid 374 through 388 Processing helix chain 'd' and resid 393 through 404 Processing helix chain 'd' and resid 409 through 416 Processing helix chain 'e' and resid 4 through 7 No H-bonds generated for 'chain 'e' and resid 4 through 7' Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 31 through 44 Processing helix chain 'e' and resid 83 through 89 Processing helix chain 'e' and resid 126 through 128 No H-bonds generated for 'chain 'e' and resid 126 through 128' Processing helix chain 'e' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU e 162 " --> pdb=" O THR e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 198 Processing helix chain 'e' and resid 213 through 221 removed outlier: 3.914A pdb=" N ARG e 221 " --> pdb=" O THR e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 255 Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 292 through 302 removed outlier: 4.273A pdb=" N ARG e 296 " --> pdb=" O ALA e 293 " (cutoff:3.500A) Proline residue: e 297 - end of helix Processing helix chain 'e' and resid 326 through 338 removed outlier: 4.683A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 352 Processing helix chain 'e' and resid 368 through 371 Processing helix chain 'e' and resid 374 through 388 Processing helix chain 'e' and resid 393 through 404 Processing helix chain 'e' and resid 409 through 416 Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 104 through 130 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 314 through 317 No H-bonds generated for 'chain 'A' and resid 314 through 317' Processing helix chain 'A' and resid 320 through 332 removed outlier: 6.294A pdb=" N ASN A 324 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 327 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 424 Processing helix chain 'A' and resid 432 through 435 No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'U' and resid 35 through 49 Processing helix chain 'U' and resid 78 through 87 Processing helix chain 'U' and resid 112 through 114 No H-bonds generated for 'chain 'U' and resid 112 through 114' Processing helix chain 'U' and resid 164 through 166 No H-bonds generated for 'chain 'U' and resid 164 through 166' Processing helix chain 'U' and resid 213 through 230 removed outlier: 3.853A pdb=" N ALA U 230 " --> pdb=" O GLU U 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 21 No H-bonds generated for 'chain 'V' and resid 19 through 21' Processing helix chain 'V' and resid 35 through 48 Processing helix chain 'V' and resid 78 through 86 Processing helix chain 'V' and resid 112 through 114 No H-bonds generated for 'chain 'V' and resid 112 through 114' Processing helix chain 'V' and resid 155 through 165 removed outlier: 4.308A pdb=" N GLU V 165 " --> pdb=" O SER V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 231 removed outlier: 4.797A pdb=" N ALA V 230 " --> pdb=" O GLU V 226 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE V 231 " --> pdb=" O GLN V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 254 No H-bonds generated for 'chain 'V' and resid 251 through 254' Processing helix chain 'V' and resid 257 through 259 No H-bonds generated for 'chain 'V' and resid 257 through 259' Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.793A pdb=" N GLU V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 281 No H-bonds generated for 'chain 'V' and resid 278 through 281' Processing helix chain 'V' and resid 286 through 288 No H-bonds generated for 'chain 'V' and resid 286 through 288' Processing helix chain 'V' and resid 297 through 308 removed outlier: 4.363A pdb=" N LEU V 307 " --> pdb=" O ILE V 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA V 308 " --> pdb=" O LYS V 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 10 No H-bonds generated for 'chain 'W' and resid 7 through 10' Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 46 through 56 Processing helix chain 'W' and resid 61 through 79 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 29 through 36 Processing helix chain 'X' and resid 43 through 45 No H-bonds generated for 'chain 'X' and resid 43 through 45' Processing helix chain 'X' and resid 50 through 54 Processing helix chain 'X' and resid 82 through 88 Processing helix chain 'X' and resid 206 through 213 removed outlier: 4.022A pdb=" N LEU X 213 " --> pdb=" O ILE X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 224 Processing helix chain 'X' and resid 271 through 280 removed outlier: 3.616A pdb=" N ASP X 280 " --> pdb=" O GLN X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 289 through 294 removed outlier: 3.847A pdb=" N GLY X 294 " --> pdb=" O GLU X 290 " (cutoff:3.500A) Processing helix chain 'X' and resid 319 through 328 Processing helix chain 'X' and resid 347 through 352 Processing helix chain 'X' and resid 359 through 370 Processing helix chain 'X' and resid 380 through 389 removed outlier: 3.720A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 399 through 408 Processing helix chain 'X' and resid 422 through 437 Processing helix chain 'X' and resid 456 through 479 removed outlier: 3.753A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 498 through 507 Processing helix chain 'X' and resid 520 through 527 Processing helix chain 'X' and resid 540 through 542 No H-bonds generated for 'chain 'X' and resid 540 through 542' Processing helix chain 'X' and resid 545 through 548 No H-bonds generated for 'chain 'X' and resid 545 through 548' Processing helix chain 'X' and resid 552 through 554 No H-bonds generated for 'chain 'X' and resid 552 through 554' Processing helix chain 'X' and resid 665 through 667 No H-bonds generated for 'chain 'X' and resid 665 through 667' Processing helix chain 'X' and resid 676 through 688 removed outlier: 3.622A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN X 688 " --> pdb=" O ASN X 684 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 711 removed outlier: 3.923A pdb=" N VAL X 708 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA X 709 " --> pdb=" O ARG X 706 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP X 711 " --> pdb=" O VAL X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 824 Processing helix chain 'X' and resid 859 through 864 removed outlier: 4.174A pdb=" N LYS X 864 " --> pdb=" O ALA X 860 " (cutoff:3.500A) Processing helix chain 'X' and resid 897 through 903 Processing helix chain 'X' and resid 943 through 979 Processing helix chain 'X' and resid 983 through 989 Processing helix chain 'X' and resid 993 through 995 No H-bonds generated for 'chain 'X' and resid 993 through 995' Processing helix chain 'X' and resid 1004 through 1037 removed outlier: 5.280A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1082 through 1084 No H-bonds generated for 'chain 'X' and resid 1082 through 1084' Processing helix chain 'X' and resid 1102 through 1105 No H-bonds generated for 'chain 'X' and resid 1102 through 1105' Processing helix chain 'X' and resid 1110 through 1132 Processing helix chain 'X' and resid 1138 through 1149 Processing helix chain 'X' and resid 1168 through 1176 Processing helix chain 'X' and resid 1192 through 1201 Processing helix chain 'X' and resid 1272 through 1280 Processing helix chain 'X' and resid 1284 through 1291 Processing helix chain 'X' and resid 1298 through 1308 Processing helix chain 'X' and resid 1321 through 1332 Processing helix chain 'Y' and resid 27 through 33 Processing helix chain 'Y' and resid 95 through 99 Processing helix chain 'Y' and resid 123 through 127 Processing helix chain 'Y' and resid 132 through 139 Processing helix chain 'Y' and resid 162 through 166 Processing helix chain 'Y' and resid 182 through 191 removed outlier: 3.770A pdb=" N SER Y 191 " --> pdb=" O ALA Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 207 Processing helix chain 'Y' and resid 212 through 229 removed outlier: 3.502A pdb=" N ALA Y 226 " --> pdb=" O LYS Y 222 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Y 227 " --> pdb=" O LEU Y 223 " (cutoff:3.500A) Processing helix chain 'Y' and resid 234 through 237 Processing helix chain 'Y' and resid 264 through 284 removed outlier: 3.843A pdb=" N ASP Y 284 " --> pdb=" O LYS Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 289 through 307 removed outlier: 4.370A pdb=" N ARG Y 293 " --> pdb=" O ASP Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 327 through 331 Processing helix chain 'Y' and resid 337 through 340 No H-bonds generated for 'chain 'Y' and resid 337 through 340' Processing helix chain 'Y' and resid 370 through 376 Processing helix chain 'Y' and resid 378 through 387 Processing helix chain 'Y' and resid 394 through 403 Processing helix chain 'Y' and resid 409 through 415 Processing helix chain 'Y' and resid 431 through 433 No H-bonds generated for 'chain 'Y' and resid 431 through 433' Processing helix chain 'Y' and resid 453 through 457 Processing helix chain 'Y' and resid 474 through 482 Processing helix chain 'Y' and resid 504 through 514 Processing helix chain 'Y' and resid 530 through 539 Processing helix chain 'Y' and resid 574 through 581 removed outlier: 4.084A pdb=" N MET Y 581 " --> pdb=" O ALA Y 577 " (cutoff:3.500A) Processing helix chain 'Y' and resid 598 through 612 Processing helix chain 'Y' and resid 615 through 635 removed outlier: 4.470A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 650 through 669 Processing helix chain 'Y' and resid 675 through 701 removed outlier: 3.838A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE Y 685 " --> pdb=" O LYS Y 681 " (cutoff:3.500A) Processing helix chain 'Y' and resid 721 through 727 Processing helix chain 'Y' and resid 734 through 741 Processing helix chain 'Y' and resid 769 through 803 removed outlier: 3.978A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 836 through 839 No H-bonds generated for 'chain 'Y' and resid 836 through 839' Processing helix chain 'Y' and resid 866 through 874 Processing helix chain 'Y' and resid 896 through 899 No H-bonds generated for 'chain 'Y' and resid 896 through 899' Processing helix chain 'Y' and resid 915 through 929 Proline residue: Y 926 - end of helix removed outlier: 4.939A pdb=" N GLN Y 929 " --> pdb=" O GLU Y 925 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1069 through 1072 No H-bonds generated for 'chain 'Y' and resid 1069 through 1072' Processing helix chain 'Y' and resid 1138 through 1146 Processing helix chain 'Y' and resid 1217 through 1224 Processing helix chain 'Y' and resid 1226 through 1244 removed outlier: 3.711A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1250 through 1260 Processing helix chain 'Y' and resid 1282 through 1294 removed outlier: 4.151A pdb=" N GLU Y1291 " --> pdb=" O ILE Y1287 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Y1292 " --> pdb=" O ALA Y1288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y1294 " --> pdb=" O ARG Y1290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1309 through 1312 No H-bonds generated for 'chain 'Y' and resid 1309 through 1312' Processing helix chain 'Y' and resid 1319 through 1323 Processing helix chain 'Y' and resid 1328 through 1338 Processing helix chain 'Y' and resid 1348 through 1352 Processing helix chain 'Y' and resid 1361 through 1372 removed outlier: 4.017A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'f' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'f' and resid 341 through 345 removed outlier: 7.621A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP f 265 " --> pdb=" O MET f 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU f 207 " --> pdb=" O ASP f 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP f 210 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER f 230 " --> pdb=" O ASP f 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 79 through 81 removed outlier: 3.704A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a' and resid 341 through 345 removed outlier: 7.622A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP a 265 " --> pdb=" O MET a 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU a 207 " --> pdb=" O ASP a 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP a 210 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER a 230 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'b' and resid 341 through 345 removed outlier: 7.621A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASP b 265 " --> pdb=" O MET b 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU b 207 " --> pdb=" O ASP b 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP b 210 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER b 230 " --> pdb=" O ASP b 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 79 through 81 removed outlier: 3.706A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 341 through 345 removed outlier: 7.621A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP c 265 " --> pdb=" O MET c 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU c 207 " --> pdb=" O ASP c 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP c 210 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER c 230 " --> pdb=" O ASP c 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'd' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 341 through 345 removed outlier: 7.621A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP d 265 " --> pdb=" O MET d 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU d 207 " --> pdb=" O ASP d 265 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ASP d 210 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER d 230 " --> pdb=" O ASP d 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'e' and resid 79 through 81 removed outlier: 3.705A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'e' and resid 341 through 345 removed outlier: 7.621A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASP e 265 " --> pdb=" O MET e 205 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU e 207 " --> pdb=" O ASP e 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ASP e 210 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER e 230 " --> pdb=" O ASP e 210 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 159 through 163 removed outlier: 3.909A pdb=" N LYS A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL A 142 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 270 through 275 Processing sheet with id= O, first strand: chain 'A' and resid 297 through 299 removed outlier: 6.452A pdb=" N GLU A 335 " --> pdb=" O MET A 305 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 24 through 28 Processing sheet with id= Q, first strand: chain 'U' and resid 170 through 172 removed outlier: 6.862A pdb=" N LYS U 145 " --> pdb=" O THR U 57 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL U 59 " --> pdb=" O ARG U 143 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG U 143 " --> pdb=" O VAL U 59 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE U 61 " --> pdb=" O SER U 141 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER U 141 " --> pdb=" O ILE U 61 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 90 through 92 Processing sheet with id= S, first strand: chain 'U' and resid 108 through 111 Processing sheet with id= T, first strand: chain 'V' and resid 23 through 28 Processing sheet with id= U, first strand: chain 'V' and resid 90 through 92 Processing sheet with id= V, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.177A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 93 through 95 Processing sheet with id= X, first strand: chain 'X' and resid 118 through 123 removed outlier: 3.964A pdb=" N SER X 72 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG X 101 " --> pdb=" O TYR X 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR X 70 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL X 103 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU X 68 " --> pdb=" O VAL X 103 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 143 through 145 Processing sheet with id= Z, first strand: chain 'X' and resid 148 through 151 Processing sheet with id= AA, first strand: chain 'X' and resid 154 through 160 removed outlier: 6.381A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 228 through 231 Processing sheet with id= AC, first strand: chain 'X' and resid 603 through 606 Processing sheet with id= AD, first strand: chain 'X' and resid 634 through 637 Processing sheet with id= AE, first strand: chain 'X' and resid 748 through 752 removed outlier: 6.463A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'X' and resid 1227 through 1232 removed outlier: 6.667A pdb=" N ILE X1096 " --> pdb=" O ALA X 803 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 830 through 839 removed outlier: 3.752A pdb=" N ASP X 930 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA X1055 " --> pdb=" O VAL X 928 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL X 928 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 1065 through 1067 Processing sheet with id= AI, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.446A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AK, first strand: chain 'Y' and resid 145 through 147 removed outlier: 4.166A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Y' and resid 350 through 354 Processing sheet with id= AM, first strand: chain 'Y' and resid 355 through 358 removed outlier: 5.956A pdb=" N ILE Y 447 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY Y 358 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU Y 449 " --> pdb=" O GLY Y 358 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'Y' and resid 365 through 369 removed outlier: 5.747A pdb=" N GLU Y 438 " --> pdb=" O CYS Y 366 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU Y 368 " --> pdb=" O GLU Y 438 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL Y 440 " --> pdb=" O LEU Y 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'Y' and resid 547 through 557 Processing sheet with id= AP, first strand: chain 'Y' and resid 819 through 823 Processing sheet with id= AQ, first strand: chain 'Y' and resid 957 through 961 removed outlier: 3.548A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id= AS, first strand: chain 'Y' and resid 1113 through 1115 removed outlier: 4.077A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG Y1036 " --> pdb=" O LYS Y1079 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS Y1079 " --> pdb=" O ARG Y1036 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Y' and resid 1162 through 1165 removed outlier: 3.749A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Y' and resid 1264 through 1266 1680 hydrogen bonds defined for protein. 4788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 20.93 Time building geometry restraints manager: 22.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16779 1.34 - 1.45: 6153 1.45 - 1.57: 29006 1.57 - 1.69: 186 1.69 - 1.81: 408 Bond restraints: 52532 Sorted by residual: bond pdb=" BE BEF a1002 " pdb=" F2 BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" BE BEF c 504 " pdb=" F2 BEF c 504 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" BE BEF c 503 " pdb=" F2 BEF c 503 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" BE BEF b1002 " pdb=" F2 BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF e1002 " pdb=" F2 BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 52527 not shown) Histogram of bond angle deviations from ideal: 82.25 - 93.01: 2 93.01 - 103.77: 912 103.77 - 114.52: 32781 114.52 - 125.28: 36854 125.28 - 136.04: 745 Bond angle restraints: 71294 Sorted by residual: angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP2 DC L 21 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP1 DC L 21 " ideal model delta sigma weight residual 108.00 84.32 23.68 3.00e+00 1.11e-01 6.23e+01 angle pdb=" CB LYS e 326 " pdb=" CG LYS e 326 " pdb=" CD LYS e 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS b 326 " pdb=" CG LYS b 326 " pdb=" CD LYS b 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS c 326 " pdb=" CG LYS c 326 " pdb=" CD LYS c 326 " ideal model delta sigma weight residual 111.30 122.87 -11.57 2.30e+00 1.89e-01 2.53e+01 ... (remaining 71289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 31381 35.23 - 70.46: 827 70.46 - 105.68: 63 105.68 - 140.91: 5 140.91 - 176.14: 7 Dihedral angle restraints: 32283 sinusoidal: 14085 harmonic: 18198 Sorted by residual: dihedral pdb=" O4' U R 24 " pdb=" C1' U R 24 " pdb=" N1 U R 24 " pdb=" C2 U R 24 " ideal model delta sinusoidal sigma weight residual 232.00 62.28 169.72 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O1B ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PB ADP b1000 " pdb=" PA ADP b1000 " ideal model delta sinusoidal sigma weight residual -60.00 102.99 -163.00 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP c 501 " pdb=" O5' ADP c 501 " pdb=" PA ADP c 501 " pdb=" O2A ADP c 501 " ideal model delta sinusoidal sigma weight residual 300.00 153.86 146.14 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 32280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 8159 0.401 - 0.802: 0 0.802 - 1.203: 0 1.203 - 1.604: 0 1.604 - 2.005: 1 Chirality restraints: 8160 Sorted by residual: chirality pdb=" P DC L 21 " pdb=" OP1 DC L 21 " pdb=" OP2 DC L 21 " pdb=" O5' DC L 21 " both_signs ideal model delta sigma weight residual True 2.35 0.34 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" P DC K -14 " pdb=" OP1 DC K -14 " pdb=" OP2 DC K -14 " pdb=" O5' DC K -14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 8157 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG L 2 " -0.026 2.00e-02 2.50e+03 1.26e-02 4.74e+00 pdb=" N9 DG L 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG L 2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG L 2 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG L 2 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG L 2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 658 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C GLU Y 658 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU Y 658 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Y 659 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU U 29 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO U 30 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO U 30 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO U 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 650 2.57 - 3.16: 42853 3.16 - 3.74: 84005 3.74 - 4.32: 111574 4.32 - 4.90: 177813 Nonbonded interactions: 416895 Sorted by model distance: nonbonded pdb="MG MG c 502 " pdb=" F3 BEF c 503 " model vdw 1.993 2.120 nonbonded pdb=" O1B ADP c 501 " pdb="MG MG c 502 " model vdw 2.008 2.170 nonbonded pdb=" O1B ADP d1000 " pdb="MG MG d1001 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP b1000 " pdb="MG MG b1001 " model vdw 2.034 2.170 nonbonded pdb=" F3 BEF c 504 " pdb="MG MG d1001 " model vdw 2.046 2.120 ... (remaining 416890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } 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: 1.570 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: 0.040 Extract box with map and model: 8.410 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 147.680 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.210 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.003 0.087 52532 Z= 0.160 Angle : 0.583 25.746 71294 Z= 0.311 Chirality : 0.046 2.005 8160 Planarity : 0.003 0.042 9006 Dihedral : 15.539 176.142 20537 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 3.45 % Allowed : 6.16 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.09), residues: 6306 helix: -1.25 (0.10), residues: 2388 sheet: -1.55 (0.15), residues: 803 loop : -2.57 (0.10), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 321 HIS 0.005 0.001 HIS c 42 PHE 0.009 0.001 PHE d 301 TYR 0.010 0.001 TYR U 177 ARG 0.002 0.000 ARG c 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 379 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 117 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (p0) REVERT: a 341 MET cc_start: 0.7891 (tpt) cc_final: 0.7195 (tpt) REVERT: b 71 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8463 (p) REVERT: d 137 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.6945 (t) REVERT: e 71 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 339 MET cc_start: 0.8552 (mmt) cc_final: 0.8076 (pmm) REVERT: W 52 ARG cc_start: 0.9315 (ttp-170) cc_final: 0.9089 (ptm160) REVERT: W 60 ASN cc_start: 0.8856 (m-40) cc_final: 0.8473 (m-40) REVERT: W 79 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7683 (pt0) REVERT: X 107 ARG cc_start: 0.6336 (mmt180) cc_final: 0.5443 (mmm160) REVERT: Y 1145 PHE cc_start: 0.7415 (m-80) cc_final: 0.7163 (m-80) REVERT: Y 1189 MET cc_start: 0.8022 (tmm) cc_final: 0.7788 (tpp) outliers start: 186 outliers final: 48 residues processed: 546 average time/residue: 0.6864 time to fit residues: 606.4814 Evaluate side-chains 310 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 9.9990 chunk 479 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 323 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 496 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 369 optimal weight: 0.8980 chunk 574 optimal weight: 0.3980 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 2 ASN f 90 ASN f 172 GLN f 361 ASN a 90 ASN a 172 GLN a 361 ASN b 2 ASN b 41 GLN b 90 ASN b 172 GLN b 361 ASN c 41 GLN c 90 ASN c 172 GLN c 361 ASN d 90 ASN d 172 GLN d 361 ASN e 90 ASN e 172 GLN e 361 ASN A 14 ASN A 129 GLN A 157 ASN A 172 ASN A 282 GLN A 324 ASN A 330 GLN V 147 GLN V 239 GLN V 276 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 ASN X 343 HIS ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 580 GLN X 618 GLN X 808 ASN X 932 GLN X1009 ASN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1017 GLN X1209 GLN X1312 ASN Y 80 HIS Y 196 GLN Y 266 ASN Y 277 ASN Y 341 ASN Y 365 GLN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 545 HIS Y 702 GLN Y 865 HIS Y1023 HIS ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52532 Z= 0.192 Angle : 0.556 25.701 71294 Z= 0.274 Chirality : 0.046 2.007 8160 Planarity : 0.003 0.056 9006 Dihedral : 12.850 177.386 8027 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 6306 helix: -0.22 (0.11), residues: 2392 sheet: -1.30 (0.15), residues: 893 loop : -2.11 (0.10), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 334 HIS 0.013 0.001 HIS e 388 PHE 0.016 0.001 PHE f 64 TYR 0.014 0.001 TYR X1231 ARG 0.012 0.000 ARG a 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 186 MET cc_start: 0.8894 (ptt) cc_final: 0.8685 (ptt) REVERT: f 327 MET cc_start: 0.8913 (ptm) cc_final: 0.8611 (ptm) REVERT: f 415 MET cc_start: 0.8361 (ppp) cc_final: 0.8127 (ppp) REVERT: b 1 MET cc_start: 0.4325 (ptt) cc_final: 0.3889 (ptt) REVERT: c 219 MET cc_start: 0.7814 (mmp) cc_final: 0.7546 (mmm) REVERT: d 327 MET cc_start: 0.8183 (ptm) cc_final: 0.7910 (ptm) REVERT: A 339 MET cc_start: 0.8658 (mmt) cc_final: 0.7984 (pmm) REVERT: A 389 MET cc_start: 0.8171 (tpt) cc_final: 0.7948 (mmm) REVERT: W 62 GLN cc_start: 0.9483 (pm20) cc_final: 0.9283 (pm20) REVERT: X 107 ARG cc_start: 0.6740 (mmt180) cc_final: 0.5931 (mmm160) REVERT: X 1230 MET cc_start: 0.6588 (tmm) cc_final: 0.6053 (tmm) REVERT: X 1243 MET cc_start: 0.7807 (tmm) cc_final: 0.7293 (tmm) REVERT: Y 1145 PHE cc_start: 0.7803 (m-80) cc_final: 0.7473 (m-80) REVERT: Y 1189 MET cc_start: 0.8154 (tmm) cc_final: 0.7839 (tpp) outliers start: 4 outliers final: 1 residues processed: 285 average time/residue: 0.7012 time to fit residues: 324.0585 Evaluate side-chains 248 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 478 optimal weight: 9.9990 chunk 391 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 575 optimal weight: 2.9990 chunk 622 optimal weight: 5.9990 chunk 512 optimal weight: 1.9990 chunk 571 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 461 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN a 2 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 135 ASN c 2 ASN c 344 HIS ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 41 GLN ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1013 GLN X1116 HIS ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 ASN Y1084 GLN Y1295 ASN ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 52532 Z= 0.269 Angle : 0.634 26.058 71294 Z= 0.317 Chirality : 0.046 2.004 8160 Planarity : 0.004 0.089 9006 Dihedral : 12.993 178.191 8027 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.06 % Allowed : 5.83 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.10), residues: 6306 helix: 0.17 (0.11), residues: 2379 sheet: -1.02 (0.16), residues: 838 loop : -1.70 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 334 HIS 0.010 0.001 HIS e 42 PHE 0.044 0.002 PHE A 24 TYR 0.035 0.002 TYR d 72 ARG 0.012 0.001 ARG W 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 270 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 405 MET cc_start: 0.9042 (ptp) cc_final: 0.8652 (ppp) REVERT: f 415 MET cc_start: 0.8550 (ppp) cc_final: 0.8327 (ppp) REVERT: a 29 MET cc_start: -0.0627 (ptt) cc_final: -0.1112 (ptt) REVERT: b 1 MET cc_start: 0.4184 (ptt) cc_final: 0.3765 (ptt) REVERT: b 21 MET cc_start: 0.6617 (tmm) cc_final: 0.5875 (tmm) REVERT: c 219 MET cc_start: 0.8099 (mmp) cc_final: 0.7726 (mmm) REVERT: d 21 MET cc_start: 0.8449 (mpp) cc_final: 0.7800 (ptp) REVERT: A 339 MET cc_start: 0.8479 (mmt) cc_final: 0.7739 (pmm) REVERT: A 389 MET cc_start: 0.8395 (tpt) cc_final: 0.7964 (tpt) REVERT: A 483 MET cc_start: 0.3744 (tmm) cc_final: 0.3243 (mmt) REVERT: W 19 LEU cc_start: 0.9422 (tt) cc_final: 0.9151 (tp) REVERT: W 52 ARG cc_start: 0.9509 (mtp85) cc_final: 0.9195 (ptm160) REVERT: X 107 ARG cc_start: 0.6703 (mmt180) cc_final: 0.5982 (tpp-160) REVERT: X 1243 MET cc_start: 0.7940 (tmm) cc_final: 0.7169 (tmm) REVERT: X 1273 MET cc_start: 0.7678 (tmm) cc_final: 0.7319 (tmm) REVERT: Y 180 MET cc_start: 0.9342 (tmm) cc_final: 0.9050 (tmm) REVERT: Y 237 MET cc_start: 0.8035 (tmm) cc_final: 0.7716 (tmm) REVERT: Y 1189 MET cc_start: 0.8355 (tmm) cc_final: 0.8007 (tpp) outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.7040 time to fit residues: 312.7059 Evaluate side-chains 235 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 6.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 5.9990 chunk 432 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 63 optimal weight: 0.1980 chunk 274 optimal weight: 0.0570 chunk 386 optimal weight: 20.0000 chunk 577 optimal weight: 30.0000 chunk 611 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 547 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 3.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 132 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 490 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 232 ASN ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 52532 Z= 0.191 Angle : 0.562 26.205 71294 Z= 0.278 Chirality : 0.046 1.999 8160 Planarity : 0.004 0.082 9006 Dihedral : 12.870 178.059 8027 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 6306 helix: 0.43 (0.11), residues: 2408 sheet: -0.87 (0.16), residues: 872 loop : -1.58 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.005 0.001 HIS X 628 PHE 0.018 0.001 PHE a 412 TYR 0.022 0.001 TYR X1229 ARG 0.012 0.000 ARG V 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 405 MET cc_start: 0.8987 (ptp) cc_final: 0.8785 (ppp) REVERT: a 21 MET cc_start: 0.7632 (mpp) cc_final: 0.7304 (mpp) REVERT: a 29 MET cc_start: -0.0803 (ptt) cc_final: -0.1219 (ptt) REVERT: b 1 MET cc_start: 0.4812 (ptt) cc_final: 0.4395 (ptt) REVERT: b 380 MET cc_start: 0.8642 (ptp) cc_final: 0.8427 (ptp) REVERT: c 219 MET cc_start: 0.8011 (mmp) cc_final: 0.7686 (mmm) REVERT: A 339 MET cc_start: 0.8529 (mmt) cc_final: 0.7764 (pmm) REVERT: A 389 MET cc_start: 0.8486 (tpt) cc_final: 0.8155 (mmt) REVERT: W 19 LEU cc_start: 0.9411 (tt) cc_final: 0.9154 (tp) REVERT: W 52 ARG cc_start: 0.9491 (mtp85) cc_final: 0.9132 (ptm160) REVERT: W 60 ASN cc_start: 0.9294 (m110) cc_final: 0.9024 (m-40) REVERT: X 107 ARG cc_start: 0.6754 (mmt180) cc_final: 0.6191 (tpp-160) REVERT: X 1273 MET cc_start: 0.8041 (tmm) cc_final: 0.7800 (tmm) REVERT: Y 151 MET cc_start: 0.5051 (ptt) cc_final: 0.4671 (pmm) REVERT: Y 237 MET cc_start: 0.8029 (tmm) cc_final: 0.7704 (tmm) REVERT: Y 1189 MET cc_start: 0.8252 (tmm) cc_final: 0.8011 (tpp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.6655 time to fit residues: 285.4641 Evaluate side-chains 232 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 5.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 0.0370 chunk 455 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 522 optimal weight: 0.7980 chunk 422 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 312 optimal weight: 0.9990 chunk 549 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 613 ASN ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 52532 Z= 0.164 Angle : 0.541 26.234 71294 Z= 0.267 Chirality : 0.046 1.998 8160 Planarity : 0.003 0.088 9006 Dihedral : 12.732 178.079 8027 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.10), residues: 6306 helix: 0.57 (0.11), residues: 2409 sheet: -0.79 (0.16), residues: 882 loop : -1.44 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 334 HIS 0.004 0.001 HIS Y 450 PHE 0.015 0.001 PHE X1144 TYR 0.016 0.001 TYR X1229 ARG 0.004 0.000 ARG W 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 5.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 415 MET cc_start: 0.8623 (ppp) cc_final: 0.8381 (ppp) REVERT: a 21 MET cc_start: 0.7636 (mpp) cc_final: 0.7261 (mpp) REVERT: a 29 MET cc_start: -0.0916 (ptt) cc_final: -0.1272 (ptt) REVERT: b 1 MET cc_start: 0.4743 (ptt) cc_final: 0.4420 (ptt) REVERT: b 21 MET cc_start: 0.4523 (ppp) cc_final: 0.4182 (ppp) REVERT: c 186 MET cc_start: 0.7547 (mtm) cc_final: 0.7225 (mtp) REVERT: c 219 MET cc_start: 0.7965 (mmp) cc_final: 0.7505 (mmm) REVERT: d 327 MET cc_start: 0.8122 (ppp) cc_final: 0.7890 (ppp) REVERT: e 245 MET cc_start: 0.8805 (ptm) cc_final: 0.8564 (ppp) REVERT: e 416 MET cc_start: 0.7670 (ptt) cc_final: 0.6938 (ptt) REVERT: A 204 MET cc_start: 0.6782 (tpt) cc_final: 0.6395 (tpt) REVERT: A 339 MET cc_start: 0.8552 (mmt) cc_final: 0.7797 (pmm) REVERT: A 389 MET cc_start: 0.8401 (tpt) cc_final: 0.8041 (mmt) REVERT: W 19 LEU cc_start: 0.9384 (tt) cc_final: 0.9133 (tp) REVERT: W 26 ARG cc_start: 0.9350 (tpt90) cc_final: 0.8735 (tpm170) REVERT: W 29 GLN cc_start: 0.9169 (mt0) cc_final: 0.8772 (mt0) REVERT: X 107 ARG cc_start: 0.6250 (mmt180) cc_final: 0.5767 (tpp-160) REVERT: X 370 MET cc_start: 0.8768 (ptp) cc_final: 0.8394 (ptp) REVERT: Y 151 MET cc_start: 0.5105 (ptt) cc_final: 0.4765 (pmm) REVERT: Y 237 MET cc_start: 0.8059 (tmm) cc_final: 0.7605 (tmm) REVERT: Y 719 PHE cc_start: 0.7095 (p90) cc_final: 0.6645 (p90) REVERT: Y 932 MET cc_start: 0.6501 (mpp) cc_final: 0.5764 (mmp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.6813 time to fit residues: 286.3883 Evaluate side-chains 231 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 6.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 20.0000 chunk 551 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 612 optimal weight: 0.5980 chunk 508 optimal weight: 20.0000 chunk 283 optimal weight: 0.0270 chunk 50 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 chunk 321 optimal weight: 0.1980 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS A 282 GLN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1268 GLN ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 52532 Z= 0.146 Angle : 0.537 26.248 71294 Z= 0.263 Chirality : 0.046 1.996 8160 Planarity : 0.003 0.067 9006 Dihedral : 12.552 178.155 8027 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.11), residues: 6306 helix: 0.70 (0.11), residues: 2402 sheet: -0.71 (0.16), residues: 887 loop : -1.36 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.003 0.001 HIS e 42 PHE 0.023 0.001 PHE c 412 TYR 0.014 0.001 TYR e 332 ARG 0.011 0.000 ARG f 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9080 (ppp) cc_final: 0.8847 (ppp) REVERT: a 29 MET cc_start: -0.0587 (ptt) cc_final: -0.0994 (ptt) REVERT: a 327 MET cc_start: 0.8705 (ptm) cc_final: 0.8207 (ppp) REVERT: b 1 MET cc_start: 0.4936 (ptt) cc_final: 0.4572 (ptt) REVERT: b 21 MET cc_start: 0.4537 (ppp) cc_final: 0.4131 (ppp) REVERT: c 21 MET cc_start: 0.7954 (ttt) cc_final: 0.7025 (ttt) REVERT: c 219 MET cc_start: 0.7945 (mmp) cc_final: 0.7491 (mmm) REVERT: d 21 MET cc_start: 0.8259 (mpp) cc_final: 0.7535 (ptp) REVERT: e 245 MET cc_start: 0.8779 (ptm) cc_final: 0.8493 (ppp) REVERT: e 416 MET cc_start: 0.7624 (ptt) cc_final: 0.6881 (ptt) REVERT: A 204 MET cc_start: 0.6831 (tpt) cc_final: 0.6475 (tpt) REVERT: A 339 MET cc_start: 0.8623 (mmt) cc_final: 0.7889 (pmm) REVERT: A 389 MET cc_start: 0.8348 (tpt) cc_final: 0.7981 (mmt) REVERT: W 19 LEU cc_start: 0.9412 (tt) cc_final: 0.9152 (tp) REVERT: W 25 ARG cc_start: 0.9218 (tpm170) cc_final: 0.8818 (tpp-160) REVERT: W 26 ARG cc_start: 0.9345 (tpt90) cc_final: 0.9119 (tpm170) REVERT: W 29 GLN cc_start: 0.9177 (mt0) cc_final: 0.8684 (mp10) REVERT: W 52 ARG cc_start: 0.9342 (ptm160) cc_final: 0.9095 (ptm160) REVERT: W 60 ASN cc_start: 0.9342 (m-40) cc_final: 0.9049 (m110) REVERT: X 107 ARG cc_start: 0.6651 (mmt180) cc_final: 0.6145 (tpp-160) REVERT: X 805 MET cc_start: 0.7782 (tmm) cc_final: 0.7424 (tmm) REVERT: X 1230 MET cc_start: 0.6693 (ppp) cc_final: 0.6238 (ppp) REVERT: X 1243 MET cc_start: 0.7247 (tpt) cc_final: 0.6729 (tpp) REVERT: Y 151 MET cc_start: 0.5128 (ptt) cc_final: 0.4761 (pmm) REVERT: Y 237 MET cc_start: 0.8051 (tmm) cc_final: 0.7537 (tmm) REVERT: Y 719 PHE cc_start: 0.6992 (p90) cc_final: 0.6584 (p90) REVERT: Y 932 MET cc_start: 0.6605 (mpp) cc_final: 0.5904 (mmp) REVERT: Y 1189 MET cc_start: 0.8706 (tpp) cc_final: 0.8451 (tpp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.7003 time to fit residues: 296.0777 Evaluate side-chains 233 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 447 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 chunk 515 optimal weight: 50.0000 chunk 341 optimal weight: 10.0000 chunk 610 optimal weight: 0.0010 chunk 381 optimal weight: 2.9990 chunk 371 optimal weight: 20.0000 chunk 281 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 2 ASN e 2 ASN e 275 ASN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1350 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 52532 Z= 0.172 Angle : 0.547 26.223 71294 Z= 0.270 Chirality : 0.046 1.997 8160 Planarity : 0.003 0.070 9006 Dihedral : 12.471 177.999 8027 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.54 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.58 (0.11), residues: 6306 helix: 0.82 (0.11), residues: 2395 sheet: -0.70 (0.17), residues: 894 loop : -1.26 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 381 HIS 0.003 0.001 HIS Y 364 PHE 0.014 0.001 PHE a 412 TYR 0.012 0.001 TYR Y 631 ARG 0.007 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 6.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9076 (ppp) cc_final: 0.8840 (ppp) REVERT: a 21 MET cc_start: 0.7770 (mpp) cc_final: 0.7366 (mpp) REVERT: a 29 MET cc_start: -0.0227 (ptt) cc_final: -0.0971 (ptt) REVERT: a 327 MET cc_start: 0.8616 (ptm) cc_final: 0.8130 (ppp) REVERT: b 21 MET cc_start: 0.4748 (ppp) cc_final: 0.4371 (ppp) REVERT: c 219 MET cc_start: 0.7983 (mmp) cc_final: 0.7540 (mmm) REVERT: d 21 MET cc_start: 0.8084 (mpp) cc_final: 0.7577 (ptp) REVERT: e 245 MET cc_start: 0.8840 (ptm) cc_final: 0.8422 (ppp) REVERT: e 390 MET cc_start: 0.8059 (pmm) cc_final: 0.7855 (pmm) REVERT: e 416 MET cc_start: 0.7624 (ptt) cc_final: 0.6880 (ptt) REVERT: A 204 MET cc_start: 0.6932 (tpt) cc_final: 0.6618 (tpt) REVERT: A 339 MET cc_start: 0.8519 (mmt) cc_final: 0.7830 (pmm) REVERT: A 389 MET cc_start: 0.8465 (tpt) cc_final: 0.8102 (mmt) REVERT: W 52 ARG cc_start: 0.9365 (ptm160) cc_final: 0.9112 (ptm160) REVERT: X 805 MET cc_start: 0.7783 (tmm) cc_final: 0.7443 (tmm) REVERT: Y 151 MET cc_start: 0.5086 (ptt) cc_final: 0.4724 (pmm) REVERT: Y 237 MET cc_start: 0.8099 (tmm) cc_final: 0.7545 (tmm) REVERT: Y 932 MET cc_start: 0.6669 (mpp) cc_final: 0.6044 (mmp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.6821 time to fit residues: 287.5430 Evaluate side-chains 226 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 364 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 387 optimal weight: 0.8980 chunk 415 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 479 optimal weight: 10.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN f 198 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52532 Z= 0.181 Angle : 0.558 26.255 71294 Z= 0.277 Chirality : 0.046 1.995 8160 Planarity : 0.003 0.062 9006 Dihedral : 12.457 178.257 8027 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.53 (0.11), residues: 6306 helix: 0.86 (0.11), residues: 2402 sheet: -0.76 (0.17), residues: 903 loop : -1.20 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 381 HIS 0.015 0.001 HIS b 42 PHE 0.013 0.001 PHE a 412 TYR 0.037 0.001 TYR X1231 ARG 0.013 0.000 ARG W 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9108 (ppp) cc_final: 0.8882 (ppp) REVERT: a 21 MET cc_start: 0.7738 (mpp) cc_final: 0.7278 (mpp) REVERT: a 29 MET cc_start: -0.0625 (ptt) cc_final: -0.1289 (ptt) REVERT: a 327 MET cc_start: 0.8582 (ptm) cc_final: 0.8150 (ppp) REVERT: b 21 MET cc_start: 0.4932 (ppp) cc_final: 0.4401 (ppp) REVERT: c 21 MET cc_start: 0.7574 (ttt) cc_final: 0.6918 (ppp) REVERT: c 219 MET cc_start: 0.7950 (mmp) cc_final: 0.7508 (mmm) REVERT: d 21 MET cc_start: 0.8063 (mpp) cc_final: 0.7563 (ptp) REVERT: e 205 MET cc_start: 0.8698 (mmm) cc_final: 0.8386 (mmm) REVERT: e 245 MET cc_start: 0.8872 (ptm) cc_final: 0.8384 (ppp) REVERT: e 416 MET cc_start: 0.7792 (ptt) cc_final: 0.7049 (ptt) REVERT: A 204 MET cc_start: 0.6996 (tpt) cc_final: 0.6505 (tpt) REVERT: A 339 MET cc_start: 0.8551 (mmt) cc_final: 0.8133 (pmm) REVERT: A 389 MET cc_start: 0.8386 (tpt) cc_final: 0.8101 (tpt) REVERT: W 19 LEU cc_start: 0.9424 (tt) cc_final: 0.9142 (tp) REVERT: W 52 ARG cc_start: 0.9413 (ptm160) cc_final: 0.9191 (ptm160) REVERT: W 60 ASN cc_start: 0.9392 (m110) cc_final: 0.9090 (m-40) REVERT: X 369 MET cc_start: 0.9214 (tmm) cc_final: 0.9013 (tmm) REVERT: X 370 MET cc_start: 0.8776 (ptp) cc_final: 0.8413 (ptp) REVERT: X 805 MET cc_start: 0.7790 (tmm) cc_final: 0.7422 (tmm) REVERT: Y 130 MET cc_start: 0.4979 (ptm) cc_final: 0.4211 (tmm) REVERT: Y 237 MET cc_start: 0.8132 (tmm) cc_final: 0.7512 (tmm) REVERT: Y 466 MET cc_start: 0.8445 (tpt) cc_final: 0.8106 (tpp) REVERT: Y 719 PHE cc_start: 0.7414 (p90) cc_final: 0.7067 (p90) REVERT: Y 932 MET cc_start: 0.6865 (mpp) cc_final: 0.6190 (mmp) REVERT: Y 1040 MET cc_start: 0.7233 (mpp) cc_final: 0.6383 (mpp) REVERT: Y 1189 MET cc_start: 0.8767 (tpp) cc_final: 0.8549 (tpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.6555 time to fit residues: 270.5064 Evaluate side-chains 224 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 7.9990 chunk 584 optimal weight: 30.0000 chunk 533 optimal weight: 5.9990 chunk 568 optimal weight: 8.9990 chunk 342 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 446 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 513 optimal weight: 0.8980 chunk 537 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 52532 Z= 0.173 Angle : 0.557 26.231 71294 Z= 0.275 Chirality : 0.046 1.991 8160 Planarity : 0.003 0.065 9006 Dihedral : 12.441 178.324 8027 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.54 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 6306 helix: 0.91 (0.11), residues: 2387 sheet: -0.70 (0.17), residues: 886 loop : -1.13 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 381 HIS 0.006 0.001 HIS X 150 PHE 0.031 0.001 PHE A 102 TYR 0.018 0.001 TYR X1231 ARG 0.006 0.000 ARG W 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9132 (ppp) cc_final: 0.8911 (ppp) REVERT: f 416 MET cc_start: 0.8541 (ptp) cc_final: 0.8333 (ptp) REVERT: a 21 MET cc_start: 0.7974 (mpp) cc_final: 0.7503 (mpp) REVERT: a 29 MET cc_start: -0.0677 (ptt) cc_final: -0.1311 (ptt) REVERT: a 327 MET cc_start: 0.8579 (ptm) cc_final: 0.8039 (ppp) REVERT: b 21 MET cc_start: 0.5188 (ppp) cc_final: 0.4638 (ppp) REVERT: c 21 MET cc_start: 0.7685 (ttt) cc_final: 0.7153 (ppp) REVERT: c 219 MET cc_start: 0.7891 (mmp) cc_final: 0.7423 (mmm) REVERT: d 21 MET cc_start: 0.8049 (mpp) cc_final: 0.7574 (ptp) REVERT: d 396 MET cc_start: 0.7818 (tpp) cc_final: 0.7553 (tpp) REVERT: e 205 MET cc_start: 0.8698 (mmm) cc_final: 0.8467 (mmm) REVERT: e 245 MET cc_start: 0.8875 (ptm) cc_final: 0.8385 (ppp) REVERT: e 416 MET cc_start: 0.7954 (ptt) cc_final: 0.7159 (ptt) REVERT: A 1 MET cc_start: 0.6846 (tpp) cc_final: 0.6624 (tpp) REVERT: A 204 MET cc_start: 0.7319 (tpt) cc_final: 0.6913 (tpt) REVERT: A 339 MET cc_start: 0.8568 (mmt) cc_final: 0.8143 (pmm) REVERT: A 389 MET cc_start: 0.8435 (tpt) cc_final: 0.8165 (tpt) REVERT: W 19 LEU cc_start: 0.9414 (tt) cc_final: 0.9147 (tp) REVERT: W 60 ASN cc_start: 0.9429 (m110) cc_final: 0.9144 (m110) REVERT: W 70 GLN cc_start: 0.9647 (mp10) cc_final: 0.9439 (mp10) REVERT: X 370 MET cc_start: 0.8786 (ptp) cc_final: 0.8436 (ptp) REVERT: X 805 MET cc_start: 0.7815 (tmm) cc_final: 0.7454 (tmm) REVERT: Y 237 MET cc_start: 0.8282 (tmm) cc_final: 0.7661 (tmm) REVERT: Y 719 PHE cc_start: 0.7301 (p90) cc_final: 0.6913 (p90) REVERT: Y 932 MET cc_start: 0.6886 (mpp) cc_final: 0.6273 (mmp) REVERT: Y 1040 MET cc_start: 0.7339 (mpp) cc_final: 0.6476 (mpp) REVERT: Y 1189 MET cc_start: 0.8764 (tpp) cc_final: 0.8559 (tpp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.6865 time to fit residues: 283.9243 Evaluate side-chains 223 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 20.0000 chunk 601 optimal weight: 30.0000 chunk 366 optimal weight: 5.9990 chunk 285 optimal weight: 0.0030 chunk 417 optimal weight: 9.9990 chunk 630 optimal weight: 20.0000 chunk 580 optimal weight: 30.0000 chunk 502 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 307 optimal weight: 8.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 HIS f 85 GLN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 ASN ** c 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN d 256 HIS e 275 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN V 23 HIS ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1008 GLN ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 52532 Z= 0.296 Angle : 0.677 26.230 71294 Z= 0.340 Chirality : 0.047 1.990 8160 Planarity : 0.005 0.226 9006 Dihedral : 12.671 178.607 8027 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.57 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 6306 helix: 0.70 (0.11), residues: 2411 sheet: -0.90 (0.17), residues: 886 loop : -1.12 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 381 HIS 0.007 0.001 HIS a 239 PHE 0.025 0.002 PHE c 412 TYR 0.019 0.002 TYR X1231 ARG 0.021 0.001 ARG X 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 5.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 21 MET cc_start: 0.7923 (mpp) cc_final: 0.7542 (mpp) REVERT: a 29 MET cc_start: -0.0806 (ptt) cc_final: -0.1363 (ptt) REVERT: a 327 MET cc_start: 0.8590 (ptm) cc_final: 0.8021 (tmm) REVERT: a 396 MET cc_start: 0.8268 (mmm) cc_final: 0.7944 (mmm) REVERT: b 21 MET cc_start: 0.6076 (ppp) cc_final: 0.5783 (ppp) REVERT: c 219 MET cc_start: 0.8157 (mmp) cc_final: 0.7690 (mmm) REVERT: d 327 MET cc_start: 0.8277 (ppp) cc_final: 0.8069 (ppp) REVERT: d 396 MET cc_start: 0.7758 (tpp) cc_final: 0.7457 (tpp) REVERT: e 205 MET cc_start: 0.8794 (mmm) cc_final: 0.8583 (mmm) REVERT: e 245 MET cc_start: 0.8745 (ptm) cc_final: 0.8530 (ppp) REVERT: e 416 MET cc_start: 0.7909 (ptt) cc_final: 0.7647 (ptt) REVERT: A 204 MET cc_start: 0.7235 (tpt) cc_final: 0.6741 (tpt) REVERT: A 339 MET cc_start: 0.8484 (mmt) cc_final: 0.8145 (pmm) REVERT: A 389 MET cc_start: 0.8463 (tpt) cc_final: 0.8155 (tpt) REVERT: W 44 ASP cc_start: 0.9359 (t70) cc_final: 0.9125 (t70) REVERT: W 60 ASN cc_start: 0.9429 (m110) cc_final: 0.9212 (m110) REVERT: X 369 MET cc_start: 0.9212 (tmm) cc_final: 0.8992 (tmm) REVERT: X 805 MET cc_start: 0.7906 (tmm) cc_final: 0.7521 (tmm) REVERT: Y 130 MET cc_start: 0.5467 (ptm) cc_final: 0.4865 (tmm) REVERT: Y 719 PHE cc_start: 0.7444 (p90) cc_final: 0.7057 (p90) REVERT: Y 932 MET cc_start: 0.6741 (mpp) cc_final: 0.6443 (mmp) REVERT: Y 1040 MET cc_start: 0.7803 (mpp) cc_final: 0.6883 (mpp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.6445 time to fit residues: 264.8676 Evaluate side-chains 222 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 0.8980 chunk 534 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 chunk 463 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 502 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 516 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** V 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.034474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.021548 restraints weight = 825632.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.022153 restraints weight = 560484.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.022456 restraints weight = 426376.462| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 52532 Z= 0.169 Angle : 0.579 26.310 71294 Z= 0.286 Chirality : 0.046 1.979 8160 Planarity : 0.003 0.062 9006 Dihedral : 12.560 179.239 8027 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.46 (0.11), residues: 6306 helix: 0.85 (0.11), residues: 2401 sheet: -0.85 (0.17), residues: 894 loop : -1.05 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 33 HIS 0.004 0.001 HIS X 150 PHE 0.022 0.001 PHE A 102 TYR 0.020 0.001 TYR X1231 ARG 0.004 0.000 ARG W 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8833.32 seconds wall clock time: 164 minutes 3.36 seconds (9843.36 seconds total)