Starting phenix.real_space_refine (version: dev) on Sun Feb 26 09:14:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2023/6q9d_4480_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 Process input model Symmetric amino acids flipped Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ARG 74": "NH1" <-> "NH2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ARG 290": "NH1" <-> "NH2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 27662 Number of models: 1 Model: "" Number of chains: 26 Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "S2" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3071 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 1 Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2402 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "A7" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 766 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Chain: "AL" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1160 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "AM" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 186 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 45.061 101.575 107.156 1.00 50.56 S ATOM 3039 SG CYSV1 405 47.158 103.730 112.929 1.00 34.82 S ATOM 2695 SG CYSV1 362 50.989 101.924 108.047 1.00 34.91 S ATOM 2676 SG CYSV1 359 47.643 107.690 107.772 1.00 39.68 S ATOM 4116 SG CYSV2 103 27.537 111.722 113.489 1.00 70.84 S ATOM 4150 SG CYSV2 108 24.797 109.674 115.838 1.00 54.73 S ATOM 4430 SG CYSV2 144 31.519 110.460 116.823 1.00 57.06 S ATOM 4453 SG CYSV2 148 29.138 108.946 119.280 1.00 58.53 S ATOM 5785 SG CYSS1 114 56.836 95.028 89.116 1.00 37.24 S ATOM 5724 SG CYSS1 105 52.106 91.870 85.861 1.00 37.49 S ATOM 5745 SG CYSS1 108 54.395 97.647 83.813 1.00 36.75 S ATOM 6117 SG CYSS1 156 57.253 103.845 96.269 1.00 30.33 S ATOM 6094 SG CYSS1 153 51.418 105.155 93.342 1.00 24.01 S ATOM 6141 SG CYSS1 159 56.181 109.633 93.549 1.00 39.39 S ATOM 6471 SG CYSS1 203 56.919 104.300 89.962 1.00 38.16 S ATOM 5230 SG CYSS1 41 58.888 102.303 102.429 1.00 41.51 S ATOM 5316 SG CYSS1 52 58.034 98.510 102.027 1.00 34.47 S ATOM 5341 SG CYSS1 55 60.631 97.385 106.673 1.00 34.04 S ATOM 5442 SG CYSS1 69 61.603 101.208 107.087 1.00 50.05 S ATOM 15784 SG CYSS7 119 66.199 68.233 63.042 1.00 43.50 S ATOM 16014 SG CYSS7 149 60.405 68.501 64.942 1.00 38.51 S ATOM 15286 SG CYSS7 55 61.667 64.666 59.661 1.00 46.73 S ATOM 15280 SG CYSS7 54 63.344 62.558 65.166 1.00 53.30 S ATOM 17206 SG CYSS8 116 57.189 76.273 64.601 1.00 30.26 S ATOM 17253 SG CYSS8 122 53.964 79.528 69.081 1.00 30.07 S ATOM 16980 SG CYSS8 87 60.476 80.149 68.961 1.00 25.40 S ATOM 17282 SG CYSS8 126 49.068 85.450 72.802 1.00 28.22 S ATOM 16953 SG CYSS8 83 55.282 85.674 70.650 1.00 23.92 S ATOM 16911 SG CYSS8 77 51.341 90.644 69.412 1.00 26.28 S ATOM 16930 SG CYSS8 80 53.224 89.233 75.620 1.00 24.55 S ATOM 18503 SG CYSS6 59 37.448 95.469 77.969 1.00 55.95 S ATOM 18681 SG CYSS6 84 41.225 97.115 77.201 1.00 48.25 S ATOM 18703 SG CYSS6 87 38.732 95.216 75.423 1.00 46.35 S Time building chain proxies: 15.13, per 1000 atoms: 0.55 Number of scatterers: 27662 At special positions: 0 Unit cell: (145.6, 158.2, 162.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 186 16.00 P 5 15.00 O 5101 8.00 N 4860 7.00 C 17481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" SF4S7 300 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" SF4S8 201 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" SF4S8 202 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " Number of angles added : 3 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 25 sheets defined 34.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 49 Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 107 through 113 Processing helix chain 'V1' and resid 115 through 129 removed outlier: 3.614A pdb=" N METV1 129 " --> pdb=" O GLYV1 125 " (cutoff:3.500A) Processing helix chain 'V1' and resid 143 through 158 Processing helix chain 'V1' and resid 166 through 168 No H-bonds generated for 'chain 'V1' and resid 166 through 168' Processing helix chain 'V1' and resid 185 through 187 No H-bonds generated for 'chain 'V1' and resid 185 through 187' Processing helix chain 'V1' and resid 191 through 196 Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.799A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 291 through 293 No H-bonds generated for 'chain 'V1' and resid 291 through 293' Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 381 Processing helix chain 'V1' and resid 386 through 399 Processing helix chain 'V1' and resid 406 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.538A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 111 Processing helix chain 'V2' and resid 113 through 124 Processing helix chain 'V2' and resid 166 through 178 Processing helix chain 'S1' and resid 13 through 15 No H-bonds generated for 'chain 'S1' and resid 13 through 15' Processing helix chain 'S1' and resid 26 through 32 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 122 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 197 through 202 removed outlier: 3.503A pdb=" N ILES1 200 " --> pdb=" O GLYS1 197 " (cutoff:3.500A) Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 273 through 275 No H-bonds generated for 'chain 'S1' and resid 273 through 275' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 326 through 338 Processing helix chain 'S1' and resid 359 through 361 No H-bonds generated for 'chain 'S1' and resid 359 through 361' Processing helix chain 'S1' and resid 369 through 373 removed outlier: 3.695A pdb=" N GLUS1 373 " --> pdb=" O GLYS1 370 " (cutoff:3.500A) Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 440 through 444 Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 624 Processing helix chain 'S1' and resid 628 through 630 No H-bonds generated for 'chain 'S1' and resid 628 through 630' Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 673 Processing helix chain 'S1' and resid 676 through 680 Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 96 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 125 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 165 through 184 Processing helix chain 'S2' and resid 208 through 228 Processing helix chain 'S2' and resid 233 through 238 Processing helix chain 'S2' and resid 247 through 252 Processing helix chain 'S2' and resid 257 through 262 Processing helix chain 'S2' and resid 269 through 272 No H-bonds generated for 'chain 'S2' and resid 269 through 272' Processing helix chain 'S2' and resid 277 through 279 No H-bonds generated for 'chain 'S2' and resid 277 through 279' Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 339 Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 4.039A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 420 Processing helix chain 'S3' and resid 17 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 137 removed outlier: 3.631A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) Processing helix chain 'S3' and resid 207 through 209 No H-bonds generated for 'chain 'S3' and resid 207 through 209' Processing helix chain 'S7' and resid 25 through 44 removed outlier: 4.092A pdb=" N SERS7 44 " --> pdb=" O ALAS7 40 " (cutoff:3.500A) Processing helix chain 'S7' and resid 55 through 61 Processing helix chain 'S7' and resid 80 through 82 No H-bonds generated for 'chain 'S7' and resid 80 through 82' Processing helix chain 'S7' and resid 94 through 105 Proline residue: S7 98 - end of helix Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 28 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 151 through 160 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 48 through 57 removed outlier: 4.596A pdb=" N PHEV3 51 " --> pdb=" O THRV3 48 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUV3 52 " --> pdb=" O TYRV3 49 " (cutoff:3.500A) Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain 'S4' and resid 19 through 21 No H-bonds generated for 'chain 'S4' and resid 19 through 21' Processing helix chain 'S4' and resid 27 through 31 Processing helix chain 'S4' and resid 49 through 51 No H-bonds generated for 'chain 'S4' and resid 49 through 51' Processing helix chain 'S4' and resid 79 through 81 No H-bonds generated for 'chain 'S4' and resid 79 through 81' Processing helix chain 'S4' and resid 89 through 99 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 78 through 84 Processing helix chain 'A9' and resid 109 through 124 Proline residue: A9 114 - end of helix Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 249 Processing helix chain 'A9' and resid 281 through 287 Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 35 Processing helix chain 'A5' and resid 42 through 60 removed outlier: 4.507A pdb=" N ALAA5 60 " --> pdb=" O SERA5 56 " (cutoff:3.500A) Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 76 through 94 removed outlier: 3.740A pdb=" N ILEA5 80 " --> pdb=" O ILEA5 76 " (cutoff:3.500A) Processing helix chain 'A6' and resid 24 through 39 Processing helix chain 'A6' and resid 42 through 48 Processing helix chain 'A6' and resid 55 through 68 Processing helix chain 'A6' and resid 75 through 93 Processing helix chain 'A6' and resid 99 through 105 Processing helix chain 'A6' and resid 117 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 9 through 17 Processing helix chain 'AL' and resid 20 through 25 removed outlier: 3.881A pdb=" N LEUAL 24 " --> pdb=" O LEUAL 20 " (cutoff:3.500A) Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 57 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing sheet with id= A, first strand: chain 'V1' and resid 220 through 224 removed outlier: 6.715A pdb=" N TYRV1 92 " --> pdb=" O THRV1 221 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALAV1 223 " --> pdb=" O TYRV1 92 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VALV1 94 " --> pdb=" O ALAV1 223 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.683A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= E, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.559A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S1' and resid 56 through 58 Processing sheet with id= G, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= I, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= J, first strand: chain 'S1' and resid 283 through 285 Processing sheet with id= K, first strand: chain 'S1' and resid 342 through 344 removed outlier: 6.480A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S1' and resid 490 through 493 removed outlier: 7.357A pdb=" N ASNS1 491 " --> pdb=" O PROS1 449 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VALS1 451 " --> pdb=" O ASNS1 491 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEUS1 493 " --> pdb=" O VALS1 451 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEUS1 453 " --> pdb=" O LEUS1 493 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VALS1 376 " --> pdb=" O METS1 450 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VALS1 452 " --> pdb=" O VALS1 376 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEUS1 378 " --> pdb=" O VALS1 452 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLYS1 454 " --> pdb=" O LEUS1 378 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VALS1 380 " --> pdb=" O GLYS1 454 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYSS1 405 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEUS1 379 " --> pdb=" O LYSS1 405 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALAS1 407 " --> pdb=" O LEUS1 379 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASPS1 420 " --> pdb=" O LEUS1 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= N, first strand: chain 'S2' and resid 361 through 369 Processing sheet with id= O, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.781A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= Q, first strand: chain 'S7' and resid 85 through 89 removed outlier: 6.229A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'S8' and resid 92 through 95 Processing sheet with id= S, first strand: chain 'S6' and resid 50 through 52 Processing sheet with id= T, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= U, first strand: chain 'S4' and resid 102 through 105 Processing sheet with id= V, first strand: chain 'S4' and resid 64 through 66 Processing sheet with id= W, first strand: chain 'A9' and resid 163 through 168 removed outlier: 6.662A pdb=" N PHEA9 129 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILEA9 166 " --> pdb=" O PHEA9 129 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HISA9 131 " --> pdb=" O ILEA9 166 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SERA9 133 " --> pdb=" O PROA9 168 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VALA9 91 " --> pdb=" O ILEA9 130 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILEA9 132 " --> pdb=" O VALA9 91 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASNA9 93 " --> pdb=" O ILEA9 132 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N HISA9 134 " --> pdb=" O ASNA9 93 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYRA9 49 " --> pdb=" O ILEA9 69 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N META9 71 " --> pdb=" O TYRA9 49 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= Y, first strand: chain 'AL' and resid 47 through 50 829 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.93 Time building geometry restraints manager: 11.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 11932 1.43 - 1.65: 16039 1.65 - 1.87: 251 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 28302 Sorted by residual: bond pdb=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.487 1.344 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.474 1.339 0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.12e+01 bond pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 1.757 1.581 0.176 3.50e-02 8.16e+02 2.52e+01 bond pdb=" O7 ZMPAA 101 " pdb=" P1 ZMPAA 101 " ideal model delta sigma weight residual 1.508 1.605 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 70.10 - 83.68: 72 83.68 - 97.26: 8 97.26 - 110.83: 9457 110.83 - 124.41: 28029 124.41 - 137.99: 790 Bond angle restraints: 38356 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 130.41 -22.67 1.95e+00 2.62e-01 1.35e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.40 12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.59 -12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.33 13.00 1.20e+00 6.94e-01 1.17e+02 angle pdb="FE1 FESV2 300 " pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.51 -12.85 1.20e+00 6.94e-01 1.15e+02 ... (remaining 38351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 16523 20.44 - 40.89: 512 40.89 - 61.33: 46 61.33 - 81.78: 15 81.78 - 102.22: 3 Dihedral angle restraints: 17099 sinusoidal: 7100 harmonic: 9999 Sorted by residual: dihedral pdb=" CA ILEA7 67 " pdb=" C ILEA7 67 " pdb=" N VALA7 68 " pdb=" CA VALA7 68 " ideal model delta harmonic sigma weight residual 180.00 126.70 53.30 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA META7 69 " pdb=" C META7 69 " pdb=" N SERA7 70 " pdb=" CA SERA7 70 " ideal model delta harmonic sigma weight residual -180.00 -132.53 -47.47 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" CA VALA7 68 " pdb=" C VALA7 68 " pdb=" N META7 69 " pdb=" CA META7 69 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 ... (remaining 17096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.227: 4153 4.227 - 8.453: 0 8.453 - 12.680: 0 12.680 - 16.906: 0 16.906 - 21.133: 24 Chirality restraints: 4177 Sorted by residual: chirality pdb="FE4 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S3 SF4S8 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S3 SF4V1 500 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " pdb=" S4 SF4S1 802 " both_signs ideal model delta sigma weight residual False -10.55 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 4174 not shown) Planarity restraints: 4957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.145 2.00e-02 2.50e+03 9.84e-02 4.60e+02 pdb=" C10 FMNV1 501 " -0.085 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.047 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.036 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.083 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.047 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.039 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.075 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.252 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.015 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.125 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.078 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.078 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.028 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.071 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.030 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.061 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.175 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALA7 68 " -0.032 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C VALA7 68 " 0.112 2.00e-02 2.50e+03 pdb=" O VALA7 68 " -0.042 2.00e-02 2.50e+03 pdb=" N META7 69 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS2 73 " -0.029 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C VALS2 73 " 0.098 2.00e-02 2.50e+03 pdb=" O VALS2 73 " -0.036 2.00e-02 2.50e+03 pdb=" N ARGS2 74 " -0.033 2.00e-02 2.50e+03 ... (remaining 4954 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 494 2.67 - 3.22: 25208 3.22 - 3.78: 42745 3.78 - 4.34: 56104 4.34 - 4.90: 91146 Nonbonded interactions: 215697 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.107 3.470 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 2.164 3.470 nonbonded pdb=" O ARGS1 243 " pdb=" O GLUS1 246 " model vdw 2.209 3.040 nonbonded pdb=" O SERS2 69 " pdb=" O METS2 72 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THRS6 12 " pdb=" O THRS6 14 " model vdw 2.231 2.440 ... (remaining 215692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 186 5.16 5 C 17481 2.51 5 N 4860 2.21 5 O 5101 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 16.300 Check model and map are aligned: 0.380 Process input model: 76.910 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.007 0.212 28302 Z= 0.462 Angle : 1.146 22.667 38356 Z= 0.628 Chirality : 1.597 21.133 4177 Planarity : 0.008 0.098 4957 Dihedral : 10.392 102.224 10665 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.77 % Favored : 89.03 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.31 % 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: -4.23 (0.11), residues: 3417 helix: -2.38 (0.10), residues: 1321 sheet: -1.91 (0.26), residues: 321 loop : -3.40 (0.12), residues: 1775 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1145 time to evaluate : 3.460 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 outliers start: 7 outliers final: 2 residues processed: 1151 average time/residue: 0.4995 time to fit residues: 868.2859 Evaluate side-chains 640 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 638 time to evaluate : 3.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2741 time to fit residues: 5.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 150 GLN V1 373 ASN V2 37 ASN V2 99 HIS ** V2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 36 GLN S1 182 GLN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 365 ASN ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 582 GLN S1 665 GLN S2 114 ASN S2 135 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 347 HIS ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN S8 157 ASN V3 75 HIS S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 37 HIS ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 216 ASN A9 288 HIS ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 49 GLN A5 72 GLN A5 82 GLN A6 125 HIS A7 50 ASN ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 72 ASN AL 116 ASN AA 35 HIS AA 47 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.248 28302 Z= 0.755 Angle : 2.398 50.758 38356 Z= 1.565 Chirality : 0.482 6.465 4177 Planarity : 0.006 0.068 4957 Dihedral : 7.006 86.314 3847 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 3417 helix: -0.89 (0.13), residues: 1340 sheet: -1.68 (0.27), residues: 312 loop : -3.10 (0.13), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 711 time to evaluate : 3.894 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 outliers start: 101 outliers final: 54 residues processed: 776 average time/residue: 0.4093 time to fit residues: 496.0860 Evaluate side-chains 654 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 600 time to evaluate : 3.316 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2553 time to fit residues: 30.3144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 308 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 274 optimal weight: 0.2980 chunk 305 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 113 HIS V2 101 GLN V2 150 ASN ** V2 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 582 GLN S2 55 HIS S2 114 ASN S2 135 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN S8 65 HIS V3 42 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 28302 Z= 0.759 Angle : 2.382 50.655 38356 Z= 1.559 Chirality : 0.479 6.351 4177 Planarity : 0.005 0.072 4957 Dihedral : 6.384 88.298 3847 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3417 helix: -0.14 (0.14), residues: 1322 sheet: -1.54 (0.27), residues: 326 loop : -2.90 (0.13), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 649 time to evaluate : 3.840 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 outliers start: 83 outliers final: 35 residues processed: 698 average time/residue: 0.4069 time to fit residues: 445.3983 Evaluate side-chains 625 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 590 time to evaluate : 3.412 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3255 time to fit residues: 24.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 304 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 179 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 46 ASN S2 116 GLN S2 190 HIS ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN S4 46 GLN S4 50 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.245 28302 Z= 0.791 Angle : 2.399 50.805 38356 Z= 1.566 Chirality : 0.479 6.357 4177 Planarity : 0.005 0.078 4957 Dihedral : 6.294 89.390 3847 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.51 % Favored : 89.46 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.14), residues: 3417 helix: 0.22 (0.14), residues: 1322 sheet: -1.55 (0.28), residues: 324 loop : -2.85 (0.13), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 601 time to evaluate : 3.450 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 outliers start: 85 outliers final: 57 residues processed: 652 average time/residue: 0.4146 time to fit residues: 423.1390 Evaluate side-chains 613 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 556 time to evaluate : 3.321 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.2671 time to fit residues: 32.0875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 243 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 226 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 167 optimal weight: 0.5980 chunk 294 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 361 GLN ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 159 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 106 GLN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN V3 44 HIS V3 55 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN S4 46 GLN A9 3 HIS ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 24 GLN A5 82 GLN AL 123 GLN AL 135 GLN ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.244 28302 Z= 0.753 Angle : 2.378 50.694 38356 Z= 1.556 Chirality : 0.479 6.376 4177 Planarity : 0.005 0.072 4957 Dihedral : 6.006 87.392 3847 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.10 % Favored : 90.87 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3417 helix: 0.47 (0.14), residues: 1324 sheet: -1.28 (0.28), residues: 318 loop : -2.70 (0.14), residues: 1775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 597 time to evaluate : 3.448 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 outliers start: 62 outliers final: 31 residues processed: 634 average time/residue: 0.4159 time to fit residues: 415.6888 Evaluate side-chains 580 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 549 time to evaluate : 3.378 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2658 time to fit residues: 19.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 272 optimal weight: 0.0870 chunk 151 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 150 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 444 GLN S1 491 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN V3 55 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 75 GLN A5 82 GLN A7 20 GLN AL 135 GLN ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.242 28302 Z= 0.755 Angle : 2.376 50.591 38356 Z= 1.555 Chirality : 0.478 6.341 4177 Planarity : 0.005 0.069 4957 Dihedral : 5.793 83.863 3847 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.57 % Favored : 90.40 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3417 helix: 0.61 (0.14), residues: 1322 sheet: -1.18 (0.28), residues: 335 loop : -2.63 (0.14), residues: 1760 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 575 time to evaluate : 3.675 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 outliers start: 43 outliers final: 25 residues processed: 598 average time/residue: 0.4215 time to fit residues: 396.8407 Evaluate side-chains 576 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 551 time to evaluate : 3.663 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2601 time to fit residues: 16.9459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 326 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 444 GLN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN S4 46 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN AL 135 GLN ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.239 28302 Z= 0.757 Angle : 2.379 50.615 38356 Z= 1.557 Chirality : 0.478 6.336 4177 Planarity : 0.005 0.068 4957 Dihedral : 5.697 80.155 3847 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3417 helix: 0.72 (0.15), residues: 1328 sheet: -1.13 (0.29), residues: 317 loop : -2.60 (0.14), residues: 1772 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 581 time to evaluate : 3.534 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 outliers start: 37 outliers final: 21 residues processed: 597 average time/residue: 0.4273 time to fit residues: 402.9725 Evaluate side-chains 561 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 540 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3055 time to fit residues: 16.0634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 98 optimal weight: 0.0770 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN A9 89 ASN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN A6 25 ASN AL 135 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.242 28302 Z= 0.784 Angle : 2.399 50.738 38356 Z= 1.565 Chirality : 0.479 6.347 4177 Planarity : 0.005 0.071 4957 Dihedral : 5.822 77.019 3847 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3417 helix: 0.63 (0.14), residues: 1336 sheet: -1.16 (0.28), residues: 355 loop : -2.70 (0.14), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 541 time to evaluate : 3.606 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 outliers start: 57 outliers final: 39 residues processed: 569 average time/residue: 0.4310 time to fit residues: 387.2958 Evaluate side-chains 554 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 515 time to evaluate : 3.702 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2543 time to fit residues: 23.0212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 2.9990 chunk 313 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 287 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN S7 106 GLN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 170 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN S4 46 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 61 GLN A5 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.238 28302 Z= 0.769 Angle : 2.396 50.753 38356 Z= 1.564 Chirality : 0.479 6.383 4177 Planarity : 0.005 0.072 4957 Dihedral : 5.818 74.443 3847 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3417 helix: 0.72 (0.15), residues: 1320 sheet: -1.21 (0.28), residues: 343 loop : -2.64 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 549 time to evaluate : 4.093 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 outliers start: 19 outliers final: 8 residues processed: 561 average time/residue: 0.4336 time to fit residues: 380.2573 Evaluate side-chains 524 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 516 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2537 time to fit residues: 8.7938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 310 optimal weight: 0.0770 chunk 268 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 444 GLN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN S7 61 HIS S7 82 GLN S7 106 GLN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 61 GLN A5 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 28302 Z= 0.755 Angle : 2.390 50.639 38356 Z= 1.560 Chirality : 0.479 6.364 4177 Planarity : 0.005 0.069 4957 Dihedral : 5.661 70.947 3847 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3417 helix: 0.77 (0.15), residues: 1326 sheet: -1.02 (0.28), residues: 349 loop : -2.59 (0.14), residues: 1742 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 557 time to evaluate : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 561 average time/residue: 0.4330 time to fit residues: 379.4803 Evaluate side-chains 535 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 527 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2726 time to fit residues: 8.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 0.0980 chunk 213 optimal weight: 0.8980 chunk 286 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 444 GLN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS S7 106 GLN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN A5 82 GLN A5 110 GLN A7 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088236 restraints weight = 61043.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090785 restraints weight = 35693.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092103 restraints weight = 23209.334| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.245 28302 Z= 0.758 Angle : 2.387 50.611 38356 Z= 1.558 Chirality : 0.478 6.351 4177 Planarity : 0.005 0.080 4957 Dihedral : 5.556 68.686 3847 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3417 helix: 0.84 (0.15), residues: 1321 sheet: -1.07 (0.28), residues: 362 loop : -2.47 (0.15), residues: 1734 =============================================================================== Job complete usr+sys time: 7352.45 seconds wall clock time: 134 minutes 3.01 seconds (8043.01 seconds total)