Starting phenix.real_space_refine (version: dev) on Thu Feb 23 18:21:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0t_14430/02_2023/7z0t_14430_updated.pdb" } resolution = 3.4 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= 0.002 sd= 1.105 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 "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C ASP 540": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 298": "OD1" <-> "OD2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E ASP 361": "OD1" <-> "OD2" Residue "E TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 196": "OD1" <-> "OD2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20634 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 4469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4469 Classifications: {'peptide': 603} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 576} Chain: "E" Number of atoms: 4244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4244 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1254 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 16, 'TRANS': 153} Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1703 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 230} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 154 Chain: "F" Number of atoms: 1075 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 136, 1064 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Conformer: "B" Number of residues, atoms: 136, 1064 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} bond proxies already assigned to first conformer: 1072 Chain: "D" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2152 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 271} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5569 Classifications: {'peptide': 714} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 682} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SEC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {' NI': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'SF4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' FE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'MGD': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6398 SG CYS E 241 55.324 69.757 67.336 1.00 47.36 S ATOM 6416 SG CYS E 244 54.861 67.666 69.020 1.00 42.40 S ATOM 8663 SG CYS E 531 57.240 67.503 66.324 1.00 37.52 S ATOM 8687 SG CYS E 534 57.045 70.207 69.541 1.00 36.91 S ATOM 6416 SG CYS E 244 54.861 67.666 69.020 1.00 42.40 S ATOM 8687 SG CYS E 534 57.045 70.207 69.541 1.00 36.91 S ATOM 8824 SG CYS B 15 50.102 119.534 90.787 1.00 12.55 S ATOM 9883 SG CYS B 159 45.238 118.056 94.102 1.00 13.28 S ATOM 8847 SG CYS B 18 46.090 115.735 88.287 1.00 14.06 S ATOM 8806 SG CYS B 12 44.558 121.787 88.338 1.00 14.97 S ATOM 9851 SG CYS B 155 42.124 110.945 91.788 1.00 15.40 S ATOM 9786 SG CYS B 146 43.163 104.965 91.763 1.00 20.72 S ATOM 8872 SG CYS B 22 45.006 107.339 86.818 1.00 15.16 S ATOM 9764 SG CYS B 143 38.376 107.564 87.895 1.00 18.05 S ATOM 9105 SG CYS B 51 33.551 107.221 84.350 1.00 20.92 S ATOM 9166 SG CYS B 59 30.352 104.091 80.022 1.00 24.47 S ATOM 9394 SG CYS B 92 32.650 109.348 78.225 1.00 21.05 S ATOM 9131 SG CYS B 54 27.912 109.750 82.999 1.00 28.60 S ATOM 9371 SG CYS B 88 35.052 102.296 75.129 1.00 19.26 S ATOM 9329 SG CYS B 82 38.456 97.362 74.978 1.00 17.92 S ATOM 9348 SG CYS B 85 33.703 98.280 70.819 1.00 17.91 S ATOM 9191 SG CYS B 63 31.708 96.800 76.322 1.00 25.12 S ATOM 10301 SG CYS G 48 54.619 75.627 62.140 1.00 55.22 S ATOM 10319 SG CYS G 51 51.949 74.672 55.551 1.00 56.70 S ATOM 10761 SG CYS G 115 54.702 79.622 59.244 1.00 30.29 S ATOM 10984 SG CYS G 145 49.153 77.410 60.250 1.00 35.48 S ATOM 11776 SG CYS F 43 34.808 97.301 64.658 1.00 18.82 S ATOM 11792 SG CYS F 46 38.913 93.712 61.961 1.00 16.74 S ATOM 11758 SG CYS F 40 34.933 96.876 58.746 1.00 23.35 S ATOM 12083 SG CYS F 85 32.728 92.357 63.068 1.00 21.20 S ATOM 11818 SG CYS F 50 45.313 88.545 61.876 1.00 17.64 S ATOM 12031 SG CYS F 78 43.063 83.430 64.511 1.00 22.40 S ATOM 12006 SG CYS F 75 43.283 83.637 57.895 1.00 18.76 S ATOM 12052 SG CYS F 81 38.839 86.589 61.372 1.00 21.92 S ATOM 12344 SG CYS F 117 36.319 117.579 66.999 1.00 35.96 S ATOM 12368 SG CYS F 120 39.893 119.007 66.424 1.00 41.03 S ATOM 12664 SG CYS F 155 38.465 116.753 69.367 1.00 28.40 S ATOM 12686 SG CYS F 158 38.420 119.327 70.020 1.00 26.22 S ATOM 15200 SG CYS A 42 56.835 118.621 92.739 1.00 14.24 S ATOM 14957 SG CYS A 8 62.214 117.800 95.806 1.00 12.65 S ATOM 15003 SG CYS A 15 58.137 120.535 99.240 1.00 12.36 S ATOM 14982 SG CYS A 11 60.747 123.231 94.584 1.00 13.62 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG F 122 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 122 " occ=0.50 Time building chain proxies: 12.56, per 1000 atoms: 0.61 Number of scatterers: 20634 At special positions: 0 Unit cell: (139.104, 173.052, 130.824, 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) Mo 1 41.97 Se 1 33.99 Ni 1 28.00 Fe 34 26.01 S 188 16.00 P 4 15.00 O 3718 8.00 N 3557 7.00 C 13130 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.05 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 800 " pdb="FE4 SF4 A 800 " - pdb=" SG CYS A 11 " pdb="FE1 SF4 A 800 " - pdb=" SG CYS A 42 " pdb="FE3 SF4 A 800 " - pdb=" SG CYS A 15 " pdb="FE2 SF4 A 800 " - pdb=" SG CYS A 8 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 15 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 12 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 18 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 143 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 22 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 146 " pdb=" SF4 B 303 " pdb="FE1 SF4 B 303 " - pdb=" SG CYS B 51 " pdb="FE3 SF4 B 303 " - pdb=" SG CYS B 92 " pdb="FE2 SF4 B 303 " - pdb=" SG CYS B 59 " pdb="FE4 SF4 B 303 " - pdb=" SG CYS B 54 " pdb=" SF4 B 304 " pdb="FE3 SF4 B 304 " - pdb=" SG CYS B 85 " pdb="FE2 SF4 B 304 " - pdb=" SG CYS B 82 " pdb="FE1 SF4 B 304 " - pdb=" SG CYS B 88 " pdb="FE4 SF4 B 304 " - pdb=" SG CYS B 63 " pdb=" SF4 F 201 " pdb="FE3 SF4 F 201 " - pdb=" SG CYS F 40 " pdb="FE4 SF4 F 201 " - pdb=" SG CYS F 85 " pdb="FE2 SF4 F 201 " - pdb=" SG CYS F 46 " pdb="FE1 SF4 F 201 " - pdb=" SG CYS F 43 " pdb=" SF4 F 202 " pdb="FE2 SF4 F 202 " - pdb=" SG CYS F 78 " pdb="FE3 SF4 F 202 " - pdb=" SG CYS F 75 " pdb="FE4 SF4 F 202 " - pdb=" SG CYS F 81 " pdb="FE1 SF4 F 202 " - pdb=" SG CYS F 50 " pdb=" SF4 G 301 " pdb="FE4 SF4 G 301 " - pdb=" SG CYS G 145 " pdb="FE2 SF4 G 301 " - pdb=" SG CYS G 51 " pdb="FE1 SF4 G 301 " - pdb=" SG CYS G 48 " pdb="FE3 SF4 G 301 " - pdb=" SG CYS G 115 " Number of angles added : 96 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 20 sheets defined 46.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'C' and resid 3 through 23 Processing helix chain 'C' and resid 29 through 56 Processing helix chain 'C' and resid 75 through 100 removed outlier: 4.006A pdb=" N ILE C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARG C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 127 through 143 Processing helix chain 'C' and resid 153 through 176 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 195 through 209 removed outlier: 3.676A pdb=" N LEU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.473A pdb=" N GLN C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 249 removed outlier: 3.804A pdb=" N LEU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 278 Processing helix chain 'C' and resid 284 through 312 removed outlier: 3.689A pdb=" N ALA C 289 " --> pdb=" O GLN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 349 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 361 through 364 No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 386 through 403 removed outlier: 4.176A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 413 through 438 removed outlier: 3.574A pdb=" N ALA C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 No H-bonds generated for 'chain 'C' and resid 446 through 449' Processing helix chain 'C' and resid 456 through 474 Processing helix chain 'C' and resid 476 through 485 Proline residue: C 481 - end of helix removed outlier: 3.544A pdb=" N ALA C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 510 through 521 Proline residue: C 514 - end of helix Processing helix chain 'C' and resid 549 through 552 No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 561 through 569 removed outlier: 4.053A pdb=" N LYS C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 580 removed outlier: 4.289A pdb=" N GLN C 580 " --> pdb=" O PRO C 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 577 through 580' Processing helix chain 'C' and resid 584 through 603 removed outlier: 3.887A pdb=" N VAL C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 42 through 51 Processing helix chain 'E' and resid 109 through 111 No H-bonds generated for 'chain 'E' and resid 109 through 111' Processing helix chain 'E' and resid 114 through 121 removed outlier: 3.783A pdb=" N ARG E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.985A pdb=" N GLU E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 245 through 259 Processing helix chain 'E' and resid 266 through 295 removed outlier: 4.008A pdb=" N MET E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 318 removed outlier: 3.551A pdb=" N MET E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 365 removed outlier: 3.577A pdb=" N ARG E 346 " --> pdb=" O MET E 342 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN E 347 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU E 364 " --> pdb=" O VAL E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 392 through 397 Processing helix chain 'E' and resid 403 through 406 No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 427 through 448 removed outlier: 3.517A pdb=" N TYR E 439 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 513 removed outlier: 4.753A pdb=" N ARG E 510 " --> pdb=" O PRO E 507 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU E 513 " --> pdb=" O ARG E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 527 Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.587A pdb=" N HIS B 26 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'G' and resid 21 through 24 No H-bonds generated for 'chain 'G' and resid 21 through 24' Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 49 through 59 removed outlier: 3.676A pdb=" N ILE G 53 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU G 54 " --> pdb=" O CYS G 51 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU G 59 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 78 No H-bonds generated for 'chain 'G' and resid 76 through 78' Processing helix chain 'G' and resid 93 through 102 Processing helix chain 'G' and resid 114 through 117 No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 132 through 134 No H-bonds generated for 'chain 'G' and resid 132 through 134' Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 205 through 219 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 236 through 251 Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 80 through 83 No H-bonds generated for 'chain 'F' and resid 80 through 83' Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 127 through 139 Processing helix chain 'F' and resid 146 through 152 removed outlier: 3.658A pdb=" N ARG F 149 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU F 150 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 164 removed outlier: 3.653A pdb=" N CYS F 163 " --> pdb=" O LYS F 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 41 through 51 Processing helix chain 'D' and resid 62 through 79 Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 98 through 117 Processing helix chain 'D' and resid 121 through 152 Proline residue: D 139 - end of helix Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 172 through 189 Processing helix chain 'D' and resid 214 through 236 removed outlier: 3.734A pdb=" N LEU D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 276 Processing helix chain 'D' and resid 288 through 306 removed outlier: 3.599A pdb=" N LEU D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 80 through 97 removed outlier: 4.026A pdb=" N LEU A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.501A pdb=" N ASP A 165 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'A' and resid 177 through 180 No H-bonds generated for 'chain 'A' and resid 177 through 180' Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 264 through 270 removed outlier: 4.671A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.759A pdb=" N ALA A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 434 through 437 No H-bonds generated for 'chain 'A' and resid 434 through 437' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.585A pdb=" N MET A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 596 through 599 No H-bonds generated for 'chain 'A' and resid 596 through 599' Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 691 through 712 removed outlier: 3.602A pdb=" N GLU A 701 " --> pdb=" O TYR A 697 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 60 through 64 removed outlier: 3.688A pdb=" N VAL C 71 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 24 through 27 removed outlier: 5.891A pdb=" N TRP E 87 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL E 35 " --> pdb=" O TRP E 87 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR E 89 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 59 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 79 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 57 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.155A pdb=" N ILE E 125 " --> pdb=" O TYR E 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 180 through 183 removed outlier: 6.424A pdb=" N ASP E 202 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE E 206 " --> pdb=" O ASP E 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 469 through 476 removed outlier: 3.562A pdb=" N ARG E 495 " --> pdb=" O MET E 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 3 through 7 Processing sheet with id= G, first strand: chain 'B' and resid 38 through 41 Processing sheet with id= H, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= I, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= J, first strand: chain 'G' and resid 70 through 72 removed outlier: 6.396A pdb=" N ALA G 38 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE G 81 " --> pdb=" O TYR G 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL G 43 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU G 83 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G 108 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE G 84 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE G 110 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL G 140 " --> pdb=" O SER G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 33 through 35 Processing sheet with id= L, first strand: chain 'F' and resid 55 through 60 Processing sheet with id= M, first strand: chain 'F' and resid 114 through 116 removed outlier: 3.746A pdb=" N ALA F 125 " --> pdb=" O CYS F 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.765A pdb=" N ARG A 28 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP A 22 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 66 through 68 Processing sheet with id= P, first strand: chain 'A' and resid 328 through 331 removed outlier: 3.525A pdb=" N GLY A 328 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 169 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 294 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE A 171 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS A 197 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 172 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 199 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET A 214 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 397 through 401 removed outlier: 6.853A pdb=" N LEU A 424 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 400 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE A 426 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 441 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP A 429 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 443 " --> pdb=" O ASP A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'A' and resid 453 through 456 removed outlier: 3.705A pdb=" N GLY A 453 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 465 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 649 through 652 removed outlier: 6.285A pdb=" N VAL A 576 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 652 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 578 " --> pdb=" O MET A 652 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 607 through 610 removed outlier: 6.351A pdb=" N ARG A 638 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 610 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN A 640 " --> pdb=" O ILE A 610 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 854 hydrogen bonds defined for protein. 2478 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: 6.68 Time building geometry restraints manager: 9.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.36: 6808 1.36 - 1.59: 13984 1.59 - 1.83: 240 1.83 - 2.06: 1 2.06 - 2.30: 96 Bond restraints: 21129 Sorted by residual: bond pdb=" N PRO A 264 " pdb=" CD PRO A 264 " ideal model delta sigma weight residual 1.473 1.342 0.131 1.40e-02 5.10e+03 8.80e+01 bond pdb=" C VAL E 362 " pdb=" O VAL E 362 " ideal model delta sigma weight residual 1.237 1.340 -0.102 1.17e-02 7.31e+03 7.66e+01 bond pdb=" C GLU A 82 " pdb=" O GLU A 82 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.32e-02 5.74e+03 5.16e+01 bond pdb=" C3 FCO E 602 " pdb="FE FCO E 602 " ideal model delta sigma weight residual 1.683 1.813 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C2 FCO E 602 " pdb="FE FCO E 602 " ideal model delta sigma weight residual 1.939 1.818 0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 21124 not shown) Histogram of bond angle deviations from ideal: 71.23 - 92.81: 100 92.81 - 114.39: 12865 114.39 - 135.96: 15850 135.96 - 157.54: 3 157.54 - 179.11: 3 Bond angle restraints: 28821 Sorted by residual: angle pdb=" C1 FCO E 602 " pdb="FE FCO E 602 " pdb=" C3 FCO E 602 " ideal model delta sigma weight residual 180.00 81.17 98.83 3.00e+00 1.11e-01 1.09e+03 angle pdb=" N THR E 517 " pdb=" CA THR E 517 " pdb=" C THR E 517 " ideal model delta sigma weight residual 113.23 152.20 -38.97 1.24e+00 6.50e-01 9.87e+02 angle pdb=" N VAL E 518 " pdb=" CA VAL E 518 " pdb=" CB VAL E 518 " ideal model delta sigma weight residual 111.23 139.08 -27.85 1.65e+00 3.67e-01 2.85e+02 angle pdb=" C ASP A 81 " pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " ideal model delta sigma weight residual 110.96 86.17 24.79 1.54e+00 4.22e-01 2.59e+02 angle pdb=" N ASP E 341 " pdb=" CA ASP E 341 " pdb=" C ASP E 341 " ideal model delta sigma weight residual 111.07 97.71 13.36 1.07e+00 8.73e-01 1.56e+02 ... (remaining 28816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 11121 17.86 - 35.73: 1068 35.73 - 53.59: 221 53.59 - 71.45: 32 71.45 - 89.32: 17 Dihedral angle restraints: 12459 sinusoidal: 4759 harmonic: 7700 Sorted by residual: dihedral pdb=" C ASP A 81 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " ideal model delta harmonic sigma weight residual -122.60 -94.59 -28.01 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N VAL E 518 " pdb=" C VAL E 518 " pdb=" CA VAL E 518 " pdb=" CB VAL E 518 " ideal model delta harmonic sigma weight residual 123.40 150.13 -26.73 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C PHE E 297 " pdb=" N PHE E 297 " pdb=" CA PHE E 297 " pdb=" CB PHE E 297 " ideal model delta harmonic sigma weight residual -122.60 -147.19 24.59 0 2.50e+00 1.60e-01 9.68e+01 ... (remaining 12456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 3250 0.299 - 0.599: 35 0.599 - 0.898: 2 0.898 - 1.197: 1 1.197 - 1.497: 5 Chirality restraints: 3293 Sorted by residual: chirality pdb=" CA THR E 517 " pdb=" N THR E 517 " pdb=" C THR E 517 " pdb=" CB THR E 517 " both_signs ideal model delta sigma weight residual False 2.53 1.03 1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb="FE4 SF4 F 201 " pdb=" S1 SF4 F 201 " pdb=" S2 SF4 F 201 " pdb=" S3 SF4 F 201 " both_signs ideal model delta sigma weight residual False 10.55 9.15 1.40 2.00e-01 2.50e+01 4.90e+01 chirality pdb="FE1 SF4 F 201 " pdb=" S2 SF4 F 201 " pdb=" S3 SF4 F 201 " pdb=" S4 SF4 F 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.20 -1.35 2.00e-01 2.50e+01 4.57e+01 ... (remaining 3290 not shown) Planarity restraints: 3661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A 801 " -0.031 2.00e-02 2.50e+03 5.59e-02 8.58e+01 pdb=" C17 MGD A 801 " 0.004 2.00e-02 2.50e+03 pdb=" C19 MGD A 801 " 0.010 2.00e-02 2.50e+03 pdb=" C21 MGD A 801 " -0.047 2.00e-02 2.50e+03 pdb=" C23 MGD A 801 " 0.140 2.00e-02 2.50e+03 pdb=" N15 MGD A 801 " -0.054 2.00e-02 2.50e+03 pdb=" N18 MGD A 801 " 0.015 2.00e-02 2.50e+03 pdb=" N19 MGD A 801 " 0.034 2.00e-02 2.50e+03 pdb=" N20 MGD A 801 " -0.024 2.00e-02 2.50e+03 pdb=" N22 MGD A 801 " -0.076 2.00e-02 2.50e+03 pdb=" O17 MGD A 801 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 268 " 0.043 2.00e-02 2.50e+03 8.50e-02 7.23e+01 pdb=" C GLU A 268 " -0.147 2.00e-02 2.50e+03 pdb=" O GLU A 268 " 0.056 2.00e-02 2.50e+03 pdb=" N ASP A 269 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 MGD A 802 " -0.031 2.00e-02 2.50e+03 4.77e-02 6.27e+01 pdb=" C17 MGD A 802 " 0.005 2.00e-02 2.50e+03 pdb=" C19 MGD A 802 " 0.009 2.00e-02 2.50e+03 pdb=" C21 MGD A 802 " -0.039 2.00e-02 2.50e+03 pdb=" C23 MGD A 802 " 0.120 2.00e-02 2.50e+03 pdb=" N15 MGD A 802 " -0.037 2.00e-02 2.50e+03 pdb=" N18 MGD A 802 " 0.019 2.00e-02 2.50e+03 pdb=" N19 MGD A 802 " 0.030 2.00e-02 2.50e+03 pdb=" N20 MGD A 802 " -0.023 2.00e-02 2.50e+03 pdb=" N22 MGD A 802 " -0.068 2.00e-02 2.50e+03 pdb=" O17 MGD A 802 " 0.015 2.00e-02 2.50e+03 ... (remaining 3658 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 5 2.18 - 2.86: 7179 2.86 - 3.54: 28952 3.54 - 4.22: 51677 4.22 - 4.90: 89479 Nonbonded interactions: 177292 Sorted by model distance: nonbonded pdb=" O GLU E 204 " pdb=" O THR E 517 " model vdw 1.499 3.040 nonbonded pdb=" O ASP A 622 " pdb=" OD1 ASP A 622 " model vdw 1.950 3.040 nonbonded pdb=" O THR D 155 " pdb=" OG1 THR D 155 " model vdw 1.976 2.440 nonbonded pdb=" OD1 ASP E 238 " pdb=" OG SER E 249 " model vdw 2.085 2.440 nonbonded pdb=" OD1 ASP E 340 " pdb=" N ASP E 341 " model vdw 2.174 2.520 ... (remaining 177287 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: 9 Type Number sf(0) Gaussians Mo 1 10.26 5 Se 1 7.20 5 Fe 34 7.16 5 Ni 1 6.56 5 P 4 5.49 5 S 188 5.16 5 C 13130 2.51 5 N 3557 2.21 5 O 3718 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 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: 25.040 Check model and map are aligned: 0.300 Process input model: 60.630 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 0.131 21129 Z= 0.478 Angle : 1.447 98.829 28821 Z= 0.882 Chirality : 0.096 1.497 3293 Planarity : 0.008 0.094 3661 Dihedral : 14.794 89.317 7521 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.42 % Favored : 95.28 % Rotamer Outliers : 1.55 % Cbeta Deviations : 1.46 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 2671 helix: -1.10 (0.13), residues: 1306 sheet: -0.82 (0.34), residues: 229 loop : -1.72 (0.17), residues: 1136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 336 time to evaluate : 2.483 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 362 average time/residue: 0.3650 time to fit residues: 198.4572 Evaluate side-chains 268 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2243 time to fit residues: 9.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 ASN C 396 GLN E 205 ASN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN B 16 HIS B 112 ASN F 148 HIS A 104 GLN A 154 ASN A 220 ASN A 321 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 21129 Z= 0.208 Angle : 0.599 9.523 28821 Z= 0.303 Chirality : 0.043 0.160 3293 Planarity : 0.005 0.061 3661 Dihedral : 5.323 66.800 2910 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2671 helix: -0.13 (0.14), residues: 1327 sheet: -0.57 (0.34), residues: 228 loop : -1.49 (0.17), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 2.522 Fit side-chains outliers start: 31 outliers final: 18 residues processed: 301 average time/residue: 0.3762 time to fit residues: 169.5805 Evaluate side-chains 272 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1940 time to fit residues: 9.7139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 328 HIS ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS D 32 HIS D 53 GLN A 23 ASN A 154 ASN A 321 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 21129 Z= 0.316 Angle : 0.622 7.813 28821 Z= 0.314 Chirality : 0.045 0.166 3293 Planarity : 0.005 0.061 3661 Dihedral : 5.294 70.408 2910 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2671 helix: 0.12 (0.14), residues: 1327 sheet: -0.57 (0.34), residues: 228 loop : -1.45 (0.17), residues: 1116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 277 time to evaluate : 2.665 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 297 average time/residue: 0.3787 time to fit residues: 170.9771 Evaluate side-chains 262 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1892 time to fit residues: 8.2846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 HIS ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 156 ASN A 154 ASN A 321 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 21129 Z= 0.194 Angle : 0.538 9.354 28821 Z= 0.270 Chirality : 0.041 0.156 3293 Planarity : 0.004 0.058 3661 Dihedral : 4.960 63.014 2910 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.78 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2671 helix: 0.45 (0.14), residues: 1324 sheet: -0.50 (0.34), residues: 225 loop : -1.37 (0.17), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 274 time to evaluate : 2.314 Fit side-chains outliers start: 29 outliers final: 11 residues processed: 292 average time/residue: 0.3649 time to fit residues: 161.8676 Evaluate side-chains 264 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 253 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2281 time to fit residues: 7.7562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 219 optimal weight: 0.5980 chunk 177 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 0.0170 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN A 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21129 Z= 0.176 Angle : 0.522 7.599 28821 Z= 0.261 Chirality : 0.041 0.153 3293 Planarity : 0.004 0.057 3661 Dihedral : 4.818 62.634 2910 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.48 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2671 helix: 0.65 (0.15), residues: 1327 sheet: -0.39 (0.35), residues: 215 loop : -1.30 (0.17), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 268 time to evaluate : 2.492 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 281 average time/residue: 0.3660 time to fit residues: 155.6654 Evaluate side-chains 258 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1833 time to fit residues: 4.5842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 119 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS C 126 ASN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21129 Z= 0.170 Angle : 0.514 7.087 28821 Z= 0.257 Chirality : 0.041 0.160 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.721 62.013 2910 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.55 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2671 helix: 0.78 (0.15), residues: 1334 sheet: -0.49 (0.35), residues: 226 loop : -1.26 (0.18), residues: 1111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 2.400 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 286 average time/residue: 0.3810 time to fit residues: 165.0945 Evaluate side-chains 267 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2283 time to fit residues: 8.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS C 126 ASN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 21129 Z= 0.203 Angle : 0.529 7.219 28821 Z= 0.264 Chirality : 0.041 0.165 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.733 62.977 2910 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2671 helix: 0.83 (0.15), residues: 1331 sheet: -0.48 (0.35), residues: 226 loop : -1.27 (0.18), residues: 1114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 258 time to evaluate : 2.460 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 266 average time/residue: 0.3942 time to fit residues: 157.8917 Evaluate side-chains 256 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 249 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2053 time to fit residues: 6.3815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.0010 chunk 49 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 101 HIS C 126 ASN ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21129 Z= 0.175 Angle : 0.515 7.174 28821 Z= 0.257 Chirality : 0.041 0.154 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.670 61.293 2910 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.48 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2671 helix: 0.92 (0.15), residues: 1327 sheet: -0.47 (0.35), residues: 226 loop : -1.23 (0.18), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 2.500 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 266 average time/residue: 0.3860 time to fit residues: 154.8102 Evaluate side-chains 251 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2619 time to fit residues: 6.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 238 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN C 550 HIS D 53 GLN A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21129 Z= 0.201 Angle : 0.532 8.864 28821 Z= 0.264 Chirality : 0.041 0.158 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.725 61.989 2910 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.18 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2671 helix: 0.84 (0.15), residues: 1335 sheet: -0.48 (0.35), residues: 226 loop : -1.24 (0.18), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 254 time to evaluate : 2.616 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 261 average time/residue: 0.3849 time to fit residues: 152.3336 Evaluate side-chains 256 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 251 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2357 time to fit residues: 5.3693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.0050 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN D 53 GLN A 228 ASN A 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21129 Z= 0.183 Angle : 0.525 7.751 28821 Z= 0.261 Chirality : 0.041 0.154 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.692 61.185 2910 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2671 helix: 0.88 (0.15), residues: 1331 sheet: -0.48 (0.35), residues: 226 loop : -1.21 (0.18), residues: 1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5342 Ramachandran restraints generated. 2671 Oldfield, 0 Emsley, 2671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 2.420 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 258 average time/residue: 0.3810 time to fit residues: 148.0773 Evaluate side-chains 249 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1842 time to fit residues: 4.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 550 HIS D 53 GLN D 228 GLN A 228 ASN A 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109433 restraints weight = 49907.080| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.86 r_work: 0.3151 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 21129 Z= 0.188 Angle : 0.530 7.819 28821 Z= 0.263 Chirality : 0.041 0.160 3293 Planarity : 0.004 0.056 3661 Dihedral : 4.695 61.177 2910 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2671 helix: 0.91 (0.15), residues: 1332 sheet: -0.46 (0.35), residues: 226 loop : -1.20 (0.18), residues: 1113 =============================================================================== Job complete usr+sys time: 4763.67 seconds wall clock time: 87 minutes 6.60 seconds (5226.60 seconds total)