Starting phenix.real_space_refine on Mon Jul 6 16:59:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z83_14541/07_2026/7z83_14541.cif" } resolution = 2.88 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 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= 0.004 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 12 5.49 5 S 267 5.16 5 C 24448 2.51 5 N 6201 2.21 5 O 6585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37546 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4741 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2475 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4637 Classifications: {'peptide': 606} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3620 Classifications: {'peptide': 478} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 204 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 68.366 59.841 192.806 1.00 4.46 S ATOM 2741 SG CYS F 357 71.773 59.423 197.325 1.00 13.98 S ATOM 3062 SG CYS F 398 66.038 56.002 197.662 1.00 14.83 S ATOM 2697 SG CYS F 351 70.624 53.556 194.145 1.00 6.41 S ATOM 4054 SG CYS E 92 78.774 51.884 213.913 1.00 41.59 S ATOM 4088 SG CYS E 97 78.972 52.551 217.454 1.00 30.20 S ATOM 4366 SG CYS E 133 73.608 51.092 213.694 1.00 38.82 S ATOM 4392 SG CYS E 137 72.860 51.860 216.950 1.00 32.41 S ATOM 5476 SG CYS G 114 78.911 66.167 175.714 1.00 5.59 S ATOM 5416 SG CYS G 105 83.999 70.096 177.071 1.00 8.84 S ATOM 5436 SG CYS G 108 84.909 64.064 174.830 1.00 5.92 S ATOM 5830 SG CYS G 156 73.198 58.342 180.322 1.00 16.09 S ATOM 5811 SG CYS G 153 79.002 57.349 183.465 1.00 19.68 S ATOM 5859 SG CYS G 159 76.372 52.710 179.965 1.00 8.57 S ATOM 6203 SG CYS G 203 78.440 57.927 176.810 1.00 3.31 S ATOM 6428 SG CYS G 230 75.560 49.588 155.665 1.00 7.51 S ATOM 6713 SG CYS G 265 75.493 45.713 160.970 1.00 11.29 S ATOM 6476 SG CYS G 237 70.213 49.098 158.682 1.00 7.08 S ATOM 6452 SG CYS G 233 72.590 43.713 155.712 1.00 23.19 S ATOM 4877 SG CYS G 36 66.779 59.213 183.065 1.00 2.92 S ATOM 4953 SG CYS G 47 68.253 62.514 183.397 1.00 7.83 S ATOM 4979 SG CYS G 50 62.468 64.137 183.260 1.00 4.89 S ATOM 5128 SG CYS G 69 61.971 60.453 182.933 1.00 8.51 S ATOM 17236 SG CYS B 129 89.070 93.729 151.930 1.00 31.62 S ATOM 16733 SG CYS B 64 94.195 97.563 153.563 1.00 30.44 S ATOM 16727 SG CYS B 63 88.618 99.611 155.364 1.00 46.19 S ATOM 17453 SG CYS B 158 90.809 93.763 157.723 1.00 40.96 S ATOM 18784 SG CYS I 102 89.476 87.911 163.774 1.00 19.96 S ATOM 18759 SG CYS I 99 95.047 86.654 160.263 1.00 10.27 S ATOM 18802 SG CYS I 105 93.574 83.248 165.558 1.00 20.35 S ATOM 18517 SG CYS I 70 89.777 82.647 160.318 1.00 12.39 S ATOM 18831 SG CYS I 109 94.635 77.775 171.830 1.00 14.15 S ATOM 18494 SG CYS I 66 92.752 77.028 165.690 1.00 14.32 S ATOM 18454 SG CYS I 60 96.886 72.777 168.034 1.00 0.00 S ATOM 18472 SG CYS I 63 90.590 73.201 170.461 1.00 11.15 S Time building chain proxies: 7.40, per 1000 atoms: 0.20 Number of scatterers: 37546 At special positions: 0 Unit cell: (154.76, 217.3, 244.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 12 15.00 O 6585 8.00 N 6201 7.00 C 24448 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8642 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 52.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.807A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.459A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 4.980A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.189A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.979A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.840A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.192A pdb=" N PHE C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.557A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.778A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.484A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.013A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.506A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.498A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.546A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.226A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.578A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.330A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.154A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.484A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.315A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.600A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1712 hydrogen bonds defined for protein. 5136 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: 5.52 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15969 1.42 - 1.64: 22012 1.64 - 1.86: 410 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38483 Sorted by residual: bond pdb=" CG PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 1.503 1.371 0.132 3.40e-02 8.65e+02 1.50e+01 bond pdb=" CB PRO N 437 " pdb=" CG PRO N 437 " ideal model delta sigma weight residual 1.492 1.678 -0.186 5.00e-02 4.00e+02 1.39e+01 bond pdb=" N PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" CA MET L 243 " pdb=" C MET L 243 " ideal model delta sigma weight residual 1.523 1.567 -0.044 1.34e-02 5.57e+03 1.07e+01 bond pdb=" N PRO N 437 " pdb=" CA PRO N 437 " ideal model delta sigma weight residual 1.466 1.418 0.048 1.50e-02 4.44e+03 1.03e+01 ... (remaining 38478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 51786 3.46 - 6.92: 340 6.92 - 10.38: 43 10.38 - 13.84: 17 13.84 - 17.30: 5 Bond angle restraints: 52191 Sorted by residual: angle pdb=" CA PRO N 437 " pdb=" N PRO N 437 " pdb=" CD PRO N 437 " ideal model delta sigma weight residual 112.00 94.70 17.30 1.40e+00 5.10e-01 1.53e+02 angle pdb=" N PRO N 437 " pdb=" CD PRO N 437 " pdb=" CG PRO N 437 " ideal model delta sigma weight residual 103.20 92.03 11.17 1.50e+00 4.44e-01 5.54e+01 angle pdb=" CB LYS C 200 " pdb=" CG LYS C 200 " pdb=" CD LYS C 200 " ideal model delta sigma weight residual 111.30 125.33 -14.03 2.30e+00 1.89e-01 3.72e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 96.68 13.13 2.21e+00 2.05e-01 3.53e+01 angle pdb=" CB LYS I 27 " pdb=" CG LYS I 27 " pdb=" CD LYS I 27 " ideal model delta sigma weight residual 111.30 124.75 -13.45 2.30e+00 1.89e-01 3.42e+01 ... (remaining 52186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 21709 34.14 - 68.27: 781 68.27 - 102.41: 55 102.41 - 136.54: 0 136.54 - 170.68: 1 Dihedral angle restraints: 22546 sinusoidal: 9033 harmonic: 13513 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 136.13 43.87 0 5.00e+00 4.00e-02 7.70e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.92 170.68 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.96 34.04 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 22543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.240: 5791 4.240 - 8.480: 0 8.480 - 12.720: 0 12.720 - 16.960: 0 16.960 - 21.200: 28 Chirality restraints: 5819 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.20 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5816 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL N 63 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.023 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO N 65 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.049 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO G 764 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.042 5.00e-02 4.00e+02 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2573 2.74 - 3.28: 37008 3.28 - 3.82: 69143 3.82 - 4.36: 83575 4.36 - 4.90: 140864 Nonbonded interactions: 333163 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.199 3.040 nonbonded pdb=" O TYR M 177 " pdb=" OG SER M 181 " model vdw 2.209 3.040 nonbonded pdb=" O TRP G 668 " pdb=" OG1 THR G 669 " model vdw 2.221 3.040 nonbonded pdb=" O ARG H 148 " pdb=" OH TYR H 294 " model vdw 2.246 3.040 nonbonded pdb=" O ARG L 516 " pdb=" OG1 THR L 520 " model vdw 2.263 3.040 ... (remaining 333158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.540 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: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.330 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 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:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 0.005 0.186 38519 Z= 0.217 Angle : 0.802 17.302 52284 Z= 0.396 Chirality : 1.466 21.200 5819 Planarity : 0.006 0.081 6516 Dihedral : 16.733 170.675 13904 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 20.62 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 4692 helix: 0.28 (0.09), residues: 2696 sheet: -0.46 (0.28), residues: 306 loop : -0.86 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 86 TYR 0.029 0.002 TYR L 428 PHE 0.040 0.002 PHE L 341 TRP 0.031 0.001 TRP L 143 HIS 0.006 0.001 HIS M 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (38483) covalent geometry : angle 0.78598 / 0.40 (52191) hydrogen bonds : bond 0.05218 / 3.50 ( 1712) hydrogen bonds : angle 4.59416 / 3.26 ( 5136) metal coordination : bond 0.05456 / 3.60 ( 36) metal coordination : angle 3.84185 / 3.01 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 440 time to evaluate : 1.402 Fit side-chains REVERT: C 160 MET cc_start: 0.9427 (mmm) cc_final: 0.9107 (mmm) REVERT: C 190 GLN cc_start: 0.8070 (mp10) cc_final: 0.7654 (mp10) REVERT: B 119 GLU cc_start: 0.8212 (mp0) cc_final: 0.7992 (mp0) REVERT: I 16 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7053 (m) REVERT: H 51 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7187 (mtp180) REVERT: H 64 MET cc_start: 0.8005 (tmm) cc_final: 0.7725 (tpt) REVERT: N 64 THR cc_start: 0.6277 (m) cc_final: 0.6064 (m) REVERT: N 135 ILE cc_start: 0.8416 (mt) cc_final: 0.8212 (tt) outliers start: 100 outliers final: 73 residues processed: 529 average time/residue: 0.6165 time to fit residues: 399.8489 Evaluate side-chains 487 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 413 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 434 THR Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 737 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 256 SER Chi-restraints excluded: chain M residue 309 THR Chi-restraints excluded: chain M residue 311 ILE Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 459 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN F 400 HIS G 57 ASN G 386 GLN G 806 GLN G 828 GLN H 138 ASN H 312 ASN A 13 HIS L 281 HIS L 411 HIS K 27 ASN K 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069146 restraints weight = 56948.034| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.29 r_work: 0.2865 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.258 38519 Z= 0.407 Angle : 2.494 53.946 52284 Z= 1.434 Chirality : 0.444 6.655 5819 Planarity : 0.005 0.071 6516 Dihedral : 7.743 173.204 5635 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 3.36 % Allowed : 18.80 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 4692 helix: 1.05 (0.10), residues: 2690 sheet: -0.33 (0.28), residues: 308 loop : -0.59 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 291 TYR 0.021 0.002 TYR N 424 PHE 0.031 0.002 PHE L 341 TRP 0.027 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.41 (38483) covalent geometry : angle 2.17769 / 1.43 (52191) hydrogen bonds : bond 0.05015 / 3.38 ( 1712) hydrogen bonds : angle 4.15585 / 2.95 ( 5136) metal coordination : bond 0.04757 / 3.14 ( 36) metal coordination : angle 28.91520 / 20.69 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 429 time to evaluate : 1.607 Fit side-chains REVERT: G 670 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 191 ASP cc_start: 0.7658 (t0) cc_final: 0.7246 (m-30) REVERT: C 200 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8821 (mmmt) REVERT: B 116 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: I 84 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8548 (p0) REVERT: H 37 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6779 (mmm-85) REVERT: H 47 TYR cc_start: 0.8561 (m-80) cc_final: 0.8261 (m-80) REVERT: M 371 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.6088 (mpp) REVERT: M 398 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7628 (tpp) REVERT: N 61 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6362 (pmm) REVERT: N 135 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7927 (tt) REVERT: N 229 ASP cc_start: 0.8586 (m-30) cc_final: 0.8303 (m-30) REVERT: K 46 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8276 (t80) outliers start: 130 outliers final: 59 residues processed: 511 average time/residue: 0.7919 time to fit residues: 487.9395 Evaluate side-chains 474 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 406 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 117 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 377 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 466 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 730 GLN G 806 GLN C 359 HIS B 58 ASN B 196 ASN H 45 ASN H 188 ASN M 490 HIS N 404 GLN K 27 ASN K 55 GLN K 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067195 restraints weight = 57036.383| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.35 r_work: 0.2811 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38519 Z= 0.424 Angle : 2.496 52.320 52284 Z= 1.435 Chirality : 0.447 6.648 5819 Planarity : 0.005 0.070 6516 Dihedral : 7.578 174.633 5568 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 4.35 % Allowed : 18.24 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4692 helix: 1.26 (0.10), residues: 2697 sheet: -0.36 (0.29), residues: 295 loop : -0.49 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 291 TYR 0.022 0.002 TYR N 424 PHE 0.031 0.002 PHE L 341 TRP 0.026 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.42 (38483) covalent geometry : angle 2.18153 / 1.43 (52191) hydrogen bonds : bond 0.05373 / 3.63 ( 1712) hydrogen bonds : angle 4.20694 / 2.99 ( 5136) metal coordination : bond 0.05821 / 3.88 ( 36) metal coordination : angle 28.84526 / 20.80 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 423 time to evaluate : 1.605 Fit side-chains REVERT: F 255 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8381 (mtt180) REVERT: G 298 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: G 643 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8539 (p) REVERT: G 670 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: G 834 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: C 127 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8428 (t80) REVERT: C 386 TRP cc_start: 0.8484 (t-100) cc_final: 0.8188 (t-100) REVERT: I 3 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7640 (tm) REVERT: H 37 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6893 (mmm-85) REVERT: H 47 TYR cc_start: 0.8603 (m-80) cc_final: 0.8218 (m-80) REVERT: H 296 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: L 200 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8213 (mtt) REVERT: M 371 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6230 (mpp) REVERT: M 398 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7650 (tpp) REVERT: N 61 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.6978 (pmm) REVERT: N 135 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7948 (tt) REVERT: N 229 ASP cc_start: 0.8632 (m-30) cc_final: 0.8340 (m-30) REVERT: K 46 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8286 (t80) outliers start: 168 outliers final: 77 residues processed: 538 average time/residue: 0.7701 time to fit residues: 502.2284 Evaluate side-chains 500 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 408 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 240 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 430 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 196 ASN F 386 GLN G 806 GLN C 236 GLN B 196 ASN H 45 ASN N 404 GLN K 27 ASN K 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068053 restraints weight = 56931.930| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.36 r_work: 0.2825 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38519 Z= 0.404 Angle : 2.493 51.273 52284 Z= 1.433 Chirality : 0.445 6.561 5819 Planarity : 0.004 0.069 6516 Dihedral : 7.470 174.497 5565 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 3.83 % Allowed : 19.40 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 4692 helix: 1.41 (0.10), residues: 2697 sheet: -0.32 (0.29), residues: 304 loop : -0.44 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 291 TYR 0.022 0.002 TYR N 424 PHE 0.029 0.001 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01158 / 0.40 (38483) covalent geometry : angle 2.17571 / 1.43 (52191) hydrogen bonds : bond 0.05099 / 3.45 ( 1712) hydrogen bonds : angle 4.14421 / 2.94 ( 5136) metal coordination : bond 0.04390 / 2.86 ( 36) metal coordination : angle 28.94878 / 20.91 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 420 time to evaluate : 1.857 Fit side-chains REVERT: F 255 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8127 (mtt180) REVERT: G 298 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: G 643 SER cc_start: 0.8851 (m) cc_final: 0.8535 (p) REVERT: G 670 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: G 828 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: G 834 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: C 127 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8438 (t80) REVERT: C 386 TRP cc_start: 0.8504 (t-100) cc_final: 0.8216 (t-100) REVERT: B 116 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: I 3 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7686 (tm) REVERT: H 37 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6945 (mmm-85) REVERT: H 47 TYR cc_start: 0.8616 (m-80) cc_final: 0.8180 (m-80) REVERT: H 296 GLN cc_start: 0.7778 (mp10) cc_final: 0.7210 (mp10) REVERT: L 107 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: L 529 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8311 (mmm160) REVERT: M 371 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.6225 (mpp) REVERT: N 61 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.6646 (pmm) REVERT: N 135 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.8004 (tt) REVERT: K 46 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8295 (t80) REVERT: J 86 GLN cc_start: 0.8032 (tp40) cc_final: 0.7511 (mm-40) outliers start: 148 outliers final: 78 residues processed: 520 average time/residue: 0.7622 time to fit residues: 481.1139 Evaluate side-chains 504 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 412 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 107 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 238 optimal weight: 7.9990 chunk 460 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 446 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 283 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN C 252 HIS B 196 ASN H 45 ASN N 404 GLN K 27 ASN K 40 ASN K 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.067990 restraints weight = 56675.890| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.37 r_work: 0.2814 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38519 Z= 0.407 Angle : 2.495 50.682 52284 Z= 1.433 Chirality : 0.444 6.566 5819 Planarity : 0.004 0.067 6516 Dihedral : 7.414 174.471 5563 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 4.68 % Allowed : 18.70 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.12), residues: 4692 helix: 1.47 (0.10), residues: 2696 sheet: -0.33 (0.29), residues: 304 loop : -0.43 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 859 TYR 0.022 0.002 TYR B 193 PHE 0.029 0.001 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.41 (38483) covalent geometry : angle 2.17745 / 1.43 (52191) hydrogen bonds : bond 0.05106 / 3.45 ( 1712) hydrogen bonds : angle 4.12777 / 2.93 ( 5136) metal coordination : bond 0.04463 / 2.92 ( 36) metal coordination : angle 28.94553 / 20.91 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 416 time to evaluate : 1.548 Fit side-chains REVERT: F 40 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: F 255 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8070 (mtt180) REVERT: G 298 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: G 643 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8579 (p) REVERT: G 670 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: G 828 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: G 834 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7708 (mp10) REVERT: C 127 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8434 (t80) REVERT: C 386 TRP cc_start: 0.8506 (t-100) cc_final: 0.8227 (t-100) REVERT: I 3 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7721 (tm) REVERT: I 84 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8525 (p0) REVERT: H 37 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6968 (mmm-85) REVERT: H 47 TYR cc_start: 0.8631 (m-80) cc_final: 0.8185 (m-80) REVERT: H 291 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7398 (mmt90) REVERT: H 296 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: M 115 PHE cc_start: 0.7914 (t80) cc_final: 0.7701 (t80) REVERT: M 371 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7752 (mmt) REVERT: M 398 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7644 (tpp) REVERT: N 61 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.6591 (pmm) REVERT: N 63 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8247 (p) REVERT: N 102 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7714 (mttm) REVERT: N 135 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7968 (tt) REVERT: K 46 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8300 (t80) REVERT: K 97 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: J 86 GLN cc_start: 0.8059 (tp40) cc_final: 0.7545 (mm-40) outliers start: 181 outliers final: 96 residues processed: 544 average time/residue: 0.7563 time to fit residues: 501.1633 Evaluate side-chains 518 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 402 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 40 LYS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 670 GLN Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 61 MET Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 395 LYS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 335 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 chunk 454 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 330 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 408 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN G 901 HIS C 135 ASN B 196 ASN N 404 GLN K 27 ASN K 55 GLN K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.068490 restraints weight = 57181.459| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.36 r_work: 0.2840 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38519 Z= 0.392 Angle : 2.492 50.674 52284 Z= 1.432 Chirality : 0.443 6.509 5819 Planarity : 0.004 0.072 6516 Dihedral : 7.284 174.063 5563 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.91 % Allowed : 19.81 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.12), residues: 4692 helix: 1.55 (0.10), residues: 2695 sheet: -0.26 (0.29), residues: 302 loop : -0.39 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 529 TYR 0.023 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.023 0.001 TRP L 143 HIS 0.009 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.39 (38483) covalent geometry : angle 2.17278 / 1.43 (52191) hydrogen bonds : bond 0.04819 / 3.25 ( 1712) hydrogen bonds : angle 4.07155 / 2.89 ( 5136) metal coordination : bond 0.03817 / 2.46 ( 36) metal coordination : angle 29.00668 / 20.94 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 418 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: F 255 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7843 (mtt180) REVERT: G 643 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 127 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 262 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7367 (mmm160) REVERT: C 386 TRP cc_start: 0.8488 (t-100) cc_final: 0.8219 (t-100) REVERT: B 116 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: I 3 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (tm) REVERT: I 84 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8524 (p0) REVERT: I 86 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8583 (ttt90) REVERT: H 37 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6955 (mmm-85) REVERT: H 47 TYR cc_start: 0.8621 (m-80) cc_final: 0.8188 (m-80) REVERT: H 296 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: M 115 PHE cc_start: 0.7900 (t80) cc_final: 0.7669 (t80) REVERT: M 304 MET cc_start: 0.8585 (tpp) cc_final: 0.8369 (mmm) REVERT: N 63 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8251 (p) REVERT: N 102 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7666 (mttm) REVERT: N 135 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7938 (tt) REVERT: N 207 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: N 229 ASP cc_start: 0.8565 (m-30) cc_final: 0.8337 (m-30) REVERT: K 27 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7780 (t160) REVERT: K 46 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8344 (t80) REVERT: K 97 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: J 86 GLN cc_start: 0.8035 (tp40) cc_final: 0.7558 (mm-40) outliers start: 151 outliers final: 85 residues processed: 522 average time/residue: 0.7629 time to fit residues: 482.3262 Evaluate side-chains 506 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 405 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 72 optimal weight: 8.9990 chunk 448 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 390 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 321 optimal weight: 0.7980 chunk 317 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN G 901 HIS B 196 ASN H 45 ASN ** N 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 27 ASN K 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068514 restraints weight = 56919.261| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.38 r_work: 0.2836 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38519 Z= 0.398 Angle : 2.495 50.680 52284 Z= 1.433 Chirality : 0.444 6.535 5819 Planarity : 0.004 0.073 6516 Dihedral : 7.241 174.083 5560 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.83 % Allowed : 19.97 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.12), residues: 4692 helix: 1.57 (0.10), residues: 2698 sheet: -0.28 (0.29), residues: 302 loop : -0.38 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 86 TYR 0.022 0.002 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.023 0.001 TRP L 143 HIS 0.009 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.40 (38483) covalent geometry : angle 2.17733 / 1.43 (52191) hydrogen bonds : bond 0.04889 / 3.30 ( 1712) hydrogen bonds : angle 4.06988 / 2.89 ( 5136) metal coordination : bond 0.04074 / 2.66 ( 36) metal coordination : angle 28.97677 / 20.93 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 412 time to evaluate : 1.576 Fit side-chains REVERT: F 255 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7829 (mtt180) REVERT: G 298 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: G 643 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (p) REVERT: C 127 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8440 (t80) REVERT: C 386 TRP cc_start: 0.8496 (t-100) cc_final: 0.8241 (t-100) REVERT: B 116 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: I 3 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7686 (tm) REVERT: I 84 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8495 (p0) REVERT: H 47 TYR cc_start: 0.8657 (m-80) cc_final: 0.8247 (m-80) REVERT: H 296 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: M 115 PHE cc_start: 0.7929 (t80) cc_final: 0.7627 (t80) REVERT: N 63 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8266 (p) REVERT: N 102 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7837 (mttm) REVERT: N 135 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7987 (tt) REVERT: N 207 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: K 46 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8292 (t80) REVERT: K 97 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: J 86 GLN cc_start: 0.8041 (tp40) cc_final: 0.7575 (mm-40) outliers start: 148 outliers final: 95 residues processed: 513 average time/residue: 0.7483 time to fit residues: 465.5277 Evaluate side-chains 518 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 409 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 855 ASN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 335 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 256 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 264 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN G 901 HIS C 252 HIS B 196 ASN H 45 ASN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 404 GLN K 27 ASN K 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.091895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067212 restraints weight = 56634.005| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.35 r_work: 0.2810 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38519 Z= 0.420 Angle : 2.501 50.763 52284 Z= 1.436 Chirality : 0.446 6.603 5819 Planarity : 0.004 0.071 6516 Dihedral : 7.421 174.417 5559 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.72 % Allowed : 20.36 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4692 helix: 1.49 (0.10), residues: 2699 sheet: -0.34 (0.29), residues: 302 loop : -0.41 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 274 TYR 0.021 0.002 TYR N 424 PHE 0.029 0.002 PHE L 341 TRP 0.024 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01188 / 0.42 (38483) covalent geometry : angle 2.18627 / 1.43 (52191) hydrogen bonds : bond 0.05234 / 3.54 ( 1712) hydrogen bonds : angle 4.14704 / 2.95 ( 5136) metal coordination : bond 0.04951 / 3.28 ( 36) metal coordination : angle 28.90401 / 20.89 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 415 time to evaluate : 1.517 Fit side-chains REVERT: F 255 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7967 (mtt180) REVERT: G 298 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: G 643 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8585 (p) REVERT: G 834 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: C 16 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8266 (tt0) REVERT: C 127 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8454 (t80) REVERT: C 307 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: C 333 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.5248 (ppp) REVERT: C 386 TRP cc_start: 0.8508 (t-100) cc_final: 0.8261 (t-100) REVERT: C 536 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8669 (ptm) REVERT: B 116 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: I 3 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7686 (tm) REVERT: I 84 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8523 (p0) REVERT: I 126 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8972 (mttt) REVERT: H 47 TYR cc_start: 0.8661 (m-80) cc_final: 0.8257 (m-80) REVERT: H 296 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: M 115 PHE cc_start: 0.7972 (t80) cc_final: 0.7699 (t80) REVERT: M 304 MET cc_start: 0.8885 (mmm) cc_final: 0.8604 (mmm) REVERT: M 398 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7636 (tpp) REVERT: N 102 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7826 (mttm) REVERT: N 135 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (tt) REVERT: N 207 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: K 97 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: J 86 GLN cc_start: 0.8075 (tp40) cc_final: 0.7857 (mm-40) outliers start: 144 outliers final: 97 residues processed: 520 average time/residue: 0.7667 time to fit residues: 483.4805 Evaluate side-chains 523 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 409 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 531 ILE Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 580 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 307 ARG Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 168 MET Chi-restraints excluded: chain L residue 247 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 398 MET Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 145 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 258 optimal weight: 4.9990 chunk 389 optimal weight: 0.0070 chunk 442 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN G 901 HIS B 196 ASN H 45 ASN N 404 GLN K 27 ASN K 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069224 restraints weight = 56976.959| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.34 r_work: 0.2852 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38519 Z= 0.389 Angle : 2.497 50.666 52284 Z= 1.433 Chirality : 0.442 6.482 5819 Planarity : 0.004 0.063 6516 Dihedral : 7.216 173.715 5559 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.08 % Allowed : 21.18 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4692 helix: 1.63 (0.10), residues: 2698 sheet: -0.24 (0.29), residues: 296 loop : -0.37 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 86 TYR 0.025 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.023 0.001 TRP L 143 HIS 0.009 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01134 / 0.39 (38483) covalent geometry : angle 2.17725 / 1.43 (52191) hydrogen bonds : bond 0.04679 / 3.16 ( 1712) hydrogen bonds : angle 4.03577 / 2.86 ( 5136) metal coordination : bond 0.03544 / 2.26 ( 36) metal coordination : angle 29.04554 / 20.94 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 422 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: F 255 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7614 (mtt180) REVERT: G 298 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: G 643 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8546 (p) REVERT: C 127 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8395 (t80) REVERT: C 386 TRP cc_start: 0.8485 (t-100) cc_final: 0.8248 (t-100) REVERT: B 116 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: I 3 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7660 (tm) REVERT: I 83 LYS cc_start: 0.8563 (mppt) cc_final: 0.8335 (mtmm) REVERT: I 86 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8763 (ttt90) REVERT: H 47 TYR cc_start: 0.8620 (m-80) cc_final: 0.8238 (m-80) REVERT: H 296 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: L 530 LEU cc_start: 0.8178 (tm) cc_final: 0.7765 (pp) REVERT: M 115 PHE cc_start: 0.7995 (t80) cc_final: 0.7672 (t80) REVERT: M 304 MET cc_start: 0.8909 (mmm) cc_final: 0.8604 (mmm) REVERT: N 102 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7704 (mttm) REVERT: N 135 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7968 (tt) REVERT: N 207 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: K 97 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: J 86 GLN cc_start: 0.8011 (tp40) cc_final: 0.7551 (mm-40) outliers start: 119 outliers final: 79 residues processed: 503 average time/residue: 0.7580 time to fit residues: 462.0319 Evaluate side-chains 499 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 408 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 437 optimal weight: 10.0000 chunk 450 optimal weight: 0.0070 chunk 314 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 136 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 415 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN C 236 GLN B 196 ASN H 45 ASN N 7 ASN N 57 GLN K 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068815 restraints weight = 56728.246| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.31 r_work: 0.2846 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38519 Z= 0.396 Angle : 2.498 50.660 52284 Z= 1.434 Chirality : 0.443 6.523 5819 Planarity : 0.004 0.069 6516 Dihedral : 7.216 173.927 5557 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.79 % Allowed : 21.50 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4692 helix: 1.63 (0.10), residues: 2700 sheet: -0.27 (0.29), residues: 302 loop : -0.34 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 86 TYR 0.023 0.002 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.023 0.001 TRP B 55 HIS 0.010 0.001 HIS G 901 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.39 (38483) covalent geometry : angle 2.18069 / 1.43 (52191) hydrogen bonds : bond 0.04796 / 3.24 ( 1712) hydrogen bonds : angle 4.04424 / 2.87 ( 5136) metal coordination : bond 0.03999 / 2.58 ( 36) metal coordination : angle 28.99247 / 20.95 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9384 Ramachandran restraints generated. 4692 Oldfield, 0 Emsley, 4692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 409 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: F 255 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7643 (mtt180) REVERT: G 298 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: G 643 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 116 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: I 3 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7689 (tm) REVERT: I 83 LYS cc_start: 0.8565 (mppt) cc_final: 0.8350 (mtmm) REVERT: H 47 TYR cc_start: 0.8649 (m-80) cc_final: 0.8215 (m-80) REVERT: H 296 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: L 530 LEU cc_start: 0.8222 (tm) cc_final: 0.7828 (pp) REVERT: M 115 PHE cc_start: 0.7990 (t80) cc_final: 0.7660 (t80) REVERT: M 304 MET cc_start: 0.8915 (mmm) cc_final: 0.8608 (mmm) REVERT: N 63 VAL cc_start: 0.8668 (p) cc_final: 0.8212 (p) REVERT: N 64 THR cc_start: 0.7086 (m) cc_final: 0.6859 (m) REVERT: N 102 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7809 (mttm) REVERT: N 135 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7972 (tt) REVERT: N 183 ASP cc_start: 0.8747 (t0) cc_final: 0.8468 (t0) REVERT: N 207 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: K 97 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: J 86 GLN cc_start: 0.8011 (tp40) cc_final: 0.7563 (mm-40) outliers start: 108 outliers final: 86 residues processed: 487 average time/residue: 0.7452 time to fit residues: 437.9845 Evaluate side-chains 499 residues out of total 3869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 403 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 255 ARG Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 411 LYS Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 550 SER Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 796 ASP Chi-restraints excluded: chain G residue 827 SER Chi-restraints excluded: chain G residue 828 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 869 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain G residue 906 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 86 ARG Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 296 GLN Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 78 ASN Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 354 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 507 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 571 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 233 VAL Chi-restraints excluded: chain M residue 275 SER Chi-restraints excluded: chain M residue 407 GLU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 292 THR Chi-restraints excluded: chain N residue 334 LEU Chi-restraints excluded: chain N residue 368 HIS Chi-restraints excluded: chain N residue 455 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 239 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 379 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 384 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN G 806 GLN B 196 ASN H 45 ASN N 404 GLN K 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.091708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066992 restraints weight = 56684.339| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.35 r_work: 0.2806 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 38519 Z= 0.427 Angle : 2.507 50.814 52284 Z= 1.438 Chirality : 0.447 6.606 5819 Planarity : 0.005 0.066 6516 Dihedral : 7.455 174.602 5557 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 21.37 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4692 helix: 1.50 (0.10), residues: 2702 sheet: -0.36 (0.29), residues: 302 loop : -0.39 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 86 TYR 0.021 0.002 TYR L 428 PHE 0.029 0.002 PHE L 341 TRP 0.027 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01200 / 0.43 (38483) covalent geometry : angle 2.19267 / 1.44 (52191) hydrogen bonds : bond 0.05321 / 3.60 ( 1712) hydrogen bonds : angle 4.17431 / 2.96 ( 5136) metal coordination : bond 0.05149 / 3.42 ( 36) metal coordination : angle 28.89114 / 20.90 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16824.10 seconds wall clock time: 286 minutes 44.59 seconds (17204.59 seconds total)