Starting phenix.real_space_refine on Tue Nov 14 12:19:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gs8_34225/11_2023/8gs8_34225_neut_updated.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 3 5.49 5 S 79 5.16 5 C 5466 2.51 5 N 1487 2.21 5 O 1592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 596": "OD1" <-> "OD2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 8637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4727 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 588} Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1920 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 13, 'TRANS': 225} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1051 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 757 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'HEM': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5204 SG CYS B 93 43.801 37.764 58.973 1.00 41.50 S ATOM 5242 SG CYS B 98 41.315 39.982 59.756 1.00 30.16 S ATOM 5258 SG CYS B 101 41.268 34.324 63.367 1.00 33.48 S ATOM 5337 SG CYS B 113 44.271 34.217 61.940 1.00 41.16 S ATOM 5991 SG CYS B 192 42.604 43.447 74.670 1.00 26.07 S ATOM 6498 SG CYS B 253 48.028 41.334 72.212 1.00 30.41 S ATOM 5952 SG CYS B 186 44.521 46.574 69.839 1.00 31.46 S ATOM 5974 SG CYS B 189 42.699 40.372 69.142 1.00 27.29 S ATOM 6420 SG CYS B 243 43.785 46.963 84.788 1.00 31.02 S ATOM 6016 SG CYS B 196 39.596 43.285 82.490 1.00 31.55 S ATOM 6467 SG CYS B 249 45.470 43.095 80.345 1.00 32.57 S Time building chain proxies: 5.54, per 1000 atoms: 0.64 Number of scatterers: 8637 At special positions: 0 Unit cell: (80.3, 83.22, 138.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 79 16.00 P 3 15.00 O 1592 8.00 N 1487 7.00 C 5466 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: 3.71 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 249 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 196 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 243 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 101 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 93 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 113 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 98 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 192 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 189 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 186 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 253 " Number of angles added : 27 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 6 sheets defined 42.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 136 through 156 Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 196 through 210 removed outlier: 3.958A pdb=" N ARG A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.648A pdb=" N ILE A 351 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.674A pdb=" N GLU A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 529 through 547 removed outlier: 4.267A pdb=" N GLU A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 547 " --> pdb=" O TYR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.664A pdb=" N LEU A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.901A pdb=" N LYS B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 248 through 252 removed outlier: 4.009A pdb=" N THR B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 252' Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 63 through 91 removed outlier: 3.625A pdb=" N HIS C 71 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 110 through 138 removed outlier: 3.769A pdb=" N HIS C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 145 through 168 removed outlier: 3.754A pdb=" N TYR C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 85 Proline residue: D 81 - end of helix removed outlier: 3.625A pdb=" N TYR D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 114 Processing helix chain 'D' and resid 118 through 145 removed outlier: 3.610A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 156 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.894A pdb=" N ILE A 244 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N HIS A 60 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG A 246 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU A 237 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA A 221 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.649A pdb=" N ALA A 64 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 90 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 66 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN A 251 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 67 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 253 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= D, first strand: chain 'A' and resid 624 through 631 removed outlier: 3.684A pdb=" N LYS A 636 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 57 through 64 Processing sheet with id= F, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.620A pdb=" N MET B 103 " --> pdb=" O THR B 110 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 987 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: 2.49 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.77: 8721 1.77 - 2.33: 119 2.33 - 2.90: 0 2.90 - 3.46: 0 3.46 - 4.03: 3 Bond restraints: 8843 Sorted by residual: bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 4.027 -1.769 2.00e-02 2.50e+03 7.82e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.770 -1.537 2.00e-02 2.50e+03 5.91e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.834 -1.534 2.00e-02 2.50e+03 5.89e+03 bond pdb=" C HIS A 99 " pdb=" N THR A 100 " ideal model delta sigma weight residual 1.335 1.230 0.104 1.25e-02 6.40e+03 6.97e+01 bond pdb=" C LEU D 101 " pdb=" N HIS D 102 " ideal model delta sigma weight residual 1.334 1.411 -0.077 1.27e-02 6.20e+03 3.66e+01 ... (remaining 8838 not shown) Histogram of bond angle deviations from ideal: 40.54 - 67.50: 9 67.50 - 94.46: 31 94.46 - 121.42: 9769 121.42 - 148.37: 2183 148.37 - 175.33: 2 Bond angle restraints: 11994 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 61.60 53.15 3.00e+00 1.11e-01 3.14e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 66.77 45.82 3.00e+00 1.11e-01 2.33e+02 angle pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 103.26 65.93 37.33 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S2 F3S B 303 " ideal model delta sigma weight residual 103.63 67.39 36.24 3.00e+00 1.11e-01 1.46e+02 angle pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 102.84 67.25 35.59 3.00e+00 1.11e-01 1.41e+02 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4704 17.51 - 35.01: 390 35.01 - 52.52: 79 52.52 - 70.03: 26 70.03 - 87.54: 14 Dihedral angle restraints: 5213 sinusoidal: 2091 harmonic: 3122 Sorted by residual: dihedral pdb=" C2C HEM D 201 " pdb=" C3C HEM D 201 " pdb=" CAC HEM D 201 " pdb=" CBC HEM D 201 " ideal model delta sinusoidal sigma weight residual 180.00 111.96 68.04 2 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CA PHE A 463 " pdb=" C PHE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA SER A 445 " pdb=" C SER A 445 " pdb=" N VAL A 446 " pdb=" CA VAL A 446 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.694: 1295 3.694 - 7.387: 0 7.387 - 11.080: 0 11.080 - 14.774: 0 14.774 - 18.467: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.70 18.47 2.00e-01 2.50e+01 8.53e+03 chirality pdb="FE1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S3 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.50 -1.06 2.00e-01 2.50e+01 2.80e+01 chirality pdb="FE3 SF4 B 302 " pdb=" S1 SF4 B 302 " pdb=" S2 SF4 B 302 " pdb=" S4 SF4 B 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.56 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 1293 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 C 201 " -0.036 2.00e-02 2.50e+03 5.08e-02 7.75e+01 pdb=" C2 UQ1 C 201 " -0.019 2.00e-02 2.50e+03 pdb=" C3 UQ1 C 201 " 0.030 2.00e-02 2.50e+03 pdb=" C4 UQ1 C 201 " -0.044 2.00e-02 2.50e+03 pdb=" C5 UQ1 C 201 " -0.013 2.00e-02 2.50e+03 pdb=" C6 UQ1 C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C7 UQ1 C 201 " 0.079 2.00e-02 2.50e+03 pdb=" CM5 UQ1 C 201 " -0.002 2.00e-02 2.50e+03 pdb=" O1 UQ1 C 201 " -0.027 2.00e-02 2.50e+03 pdb=" O2 UQ1 C 201 " -0.035 2.00e-02 2.50e+03 pdb=" O3 UQ1 C 201 " 0.117 2.00e-02 2.50e+03 pdb=" O4 UQ1 C 201 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBA HEM D 201 " 0.036 2.00e-02 2.50e+03 7.81e-02 6.11e+01 pdb=" CGA HEM D 201 " -0.135 2.00e-02 2.50e+03 pdb=" O1A HEM D 201 " 0.050 2.00e-02 2.50e+03 pdb=" O2A HEM D 201 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM D 201 " 0.029 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" CGD HEM D 201 " -0.102 2.00e-02 2.50e+03 pdb=" O1D HEM D 201 " 0.036 2.00e-02 2.50e+03 pdb=" O2D HEM D 201 " 0.036 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 508 2.71 - 3.26: 8837 3.26 - 3.81: 14751 3.81 - 4.35: 20163 4.35 - 4.90: 32618 Nonbonded interactions: 76877 Sorted by model distance: nonbonded pdb=" O GLN A 104 " pdb=" O4 FAD A 701 " model vdw 2.168 3.040 nonbonded pdb=" NE2 HIS C 127 " pdb="FE HEM D 201 " model vdw 2.224 3.080 nonbonded pdb=" S3 F3S B 303 " pdb="FE3 F3S B 303 " model vdw 2.256 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.256 2.688 nonbonded pdb=" S4 F3S B 303 " pdb="FE4 F3S B 303 " model vdw 2.265 2.688 ... (remaining 76872 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 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 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: 15.100 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: 0.000 Extract box with map and model: 14.200 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.650 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.032 1.769 8843 Z= 2.172 Angle : 1.670 53.152 11994 Z= 0.853 Chirality : 0.520 18.467 1296 Planarity : 0.013 0.135 1518 Dihedral : 14.564 87.536 3225 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 0.67 % Allowed : 1.11 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.22 (0.21), residues: 1082 helix: -3.21 (0.17), residues: 487 sheet: -2.15 (0.46), residues: 97 loop : -2.35 (0.25), residues: 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 118 average time/residue: 1.2295 time to fit residues: 155.0964 Evaluate side-chains 93 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.1108 time to fit residues: 2.4743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 155 ASN A 185 GLN A 650 ASN B 66 ASN B 81 ASN B 120 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 8843 Z= 0.268 Angle : 1.244 79.819 11994 Z= 0.471 Chirality : 0.043 0.469 1296 Planarity : 0.005 0.062 1518 Dihedral : 7.787 86.414 1247 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.40 % Favored : 97.50 % Rotamer: Outliers : 1.56 % Allowed : 6.44 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.24), residues: 1082 helix: -0.43 (0.22), residues: 484 sheet: -1.37 (0.48), residues: 96 loop : -1.40 (0.27), residues: 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 99 average time/residue: 1.1285 time to fit residues: 120.2747 Evaluate side-chains 98 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.1646 time to fit residues: 2.1770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN A 650 ASN B 81 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 8843 Z= 0.427 Angle : 1.252 76.884 11994 Z= 0.479 Chirality : 0.049 0.654 1296 Planarity : 0.005 0.054 1518 Dihedral : 7.626 81.223 1247 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.56 % Allowed : 9.00 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.26), residues: 1082 helix: 0.63 (0.23), residues: 495 sheet: -0.99 (0.49), residues: 96 loop : -0.92 (0.29), residues: 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 1.1325 time to fit residues: 122.0502 Evaluate side-chains 97 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.1692 time to fit residues: 2.3182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 8843 Z= 0.274 Angle : 1.076 58.210 11994 Z= 0.407 Chirality : 0.066 1.906 1296 Planarity : 0.004 0.051 1518 Dihedral : 7.049 81.616 1247 Min Nonbonded Distance : 1.544 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.66 % Favored : 98.24 % Rotamer: Outliers : 1.89 % Allowed : 10.56 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.26), residues: 1082 helix: 1.33 (0.24), residues: 496 sheet: -0.72 (0.50), residues: 98 loop : -0.81 (0.30), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 105 average time/residue: 1.1615 time to fit residues: 131.0124 Evaluate side-chains 96 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.2016 time to fit residues: 2.0929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 8843 Z= 0.270 Angle : 1.028 83.370 11994 Z= 0.395 Chirality : 0.059 1.528 1296 Planarity : 0.004 0.049 1518 Dihedral : 6.919 77.510 1247 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.89 % Allowed : 11.22 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.26), residues: 1082 helix: 1.41 (0.24), residues: 502 sheet: -0.53 (0.50), residues: 98 loop : -0.80 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.033 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 1.0678 time to fit residues: 117.7524 Evaluate side-chains 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1646 time to fit residues: 2.1439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 8843 Z= 0.372 Angle : 1.057 82.827 11994 Z= 0.415 Chirality : 0.062 1.564 1296 Planarity : 0.005 0.048 1518 Dihedral : 6.991 71.328 1247 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.89 % Allowed : 12.00 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.26), residues: 1082 helix: 1.29 (0.24), residues: 502 sheet: -0.36 (0.51), residues: 96 loop : -0.81 (0.29), residues: 484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.989 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 101 average time/residue: 1.1212 time to fit residues: 122.0285 Evaluate side-chains 93 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.4044 time to fit residues: 3.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8843 Z= 0.230 Angle : 1.007 81.608 11994 Z= 0.386 Chirality : 0.060 1.587 1296 Planarity : 0.004 0.048 1518 Dihedral : 6.680 72.436 1247 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 13.56 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.26), residues: 1082 helix: 1.54 (0.24), residues: 505 sheet: -0.30 (0.50), residues: 98 loop : -0.77 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.996 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 1.0817 time to fit residues: 111.2614 Evaluate side-chains 91 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.2298 time to fit residues: 1.8903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 8843 Z= 0.325 Angle : 1.035 81.122 11994 Z= 0.403 Chirality : 0.062 1.616 1296 Planarity : 0.004 0.047 1518 Dihedral : 6.778 68.410 1247 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.22 % Allowed : 14.11 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.26), residues: 1082 helix: 1.41 (0.24), residues: 502 sheet: -0.21 (0.51), residues: 96 loop : -0.74 (0.29), residues: 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.981 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 1.1056 time to fit residues: 107.3682 Evaluate side-chains 97 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.5087 time to fit residues: 3.1182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8843 Z= 0.260 Angle : 1.013 81.002 11994 Z= 0.389 Chirality : 0.060 1.580 1296 Planarity : 0.004 0.047 1518 Dihedral : 6.611 68.538 1247 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.00 % Allowed : 14.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1082 helix: 1.59 (0.24), residues: 504 sheet: -0.14 (0.50), residues: 98 loop : -0.74 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.984 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 94 average time/residue: 1.2063 time to fit residues: 121.5957 Evaluate side-chains 90 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1887 time to fit residues: 2.0154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8843 Z= 0.274 Angle : 1.021 80.943 11994 Z= 0.395 Chirality : 0.061 1.584 1296 Planarity : 0.004 0.047 1518 Dihedral : 6.627 67.217 1247 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.89 % Allowed : 14.78 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1082 helix: 1.56 (0.24), residues: 503 sheet: -0.10 (0.50), residues: 98 loop : -0.74 (0.29), residues: 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 1.080 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 1.2246 time to fit residues: 117.3555 Evaluate side-chains 87 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.3390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112623 restraints weight = 8976.128| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.86 r_work: 0.2972 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8843 Z= 0.203 Angle : 0.998 81.220 11994 Z= 0.380 Chirality : 0.059 1.556 1296 Planarity : 0.004 0.047 1518 Dihedral : 6.404 67.746 1247 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.78 % Allowed : 15.11 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.26), residues: 1082 helix: 1.61 (0.24), residues: 518 sheet: 0.16 (0.50), residues: 96 loop : -0.70 (0.30), residues: 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.84 seconds wall clock time: 54 minutes 16.54 seconds (3256.54 seconds total)