Starting phenix.real_space_refine on Sun Aug 11 05:11:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy8_37919/08_2024/8wy8_37919.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 20363 2.51 5 N 5069 2.21 5 O 5856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A ASP 776": "OD1" <-> "OD2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C ASP 547": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 624": "OE1" <-> "OE2" Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 674": "OD1" <-> "OD2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "C TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 777": "OD1" <-> "OD2" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 945": "OD1" <-> "OD2" Residue "C PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 553": "OD1" <-> "OD2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 662": "OD1" <-> "OD2" Residue "D PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 784": "OE1" <-> "OE2" Residue "D TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7880 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 19, 'TRANS': 923} Chain breaks: 7 Chain: "B" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7869 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 19, 'TRANS': 920} Chain breaks: 7 Chain: "C" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7869 Classifications: {'peptide': 942} Link IDs: {'PTRANS': 19, 'TRANS': 922} Chain breaks: 8 Chain: "D" Number of atoms: 7794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7794 Classifications: {'peptide': 932} Link IDs: {'PTRANS': 19, 'TRANS': 912} Chain breaks: 8 Time building chain proxies: 16.67, per 1000 atoms: 0.53 Number of scatterers: 31412 At special positions: 0 Unit cell: (100.894, 127.358, 265.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5856 8.00 N 5069 7.00 C 20363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.68 Conformation dependent library (CDL) restraints added in 5.1 seconds 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 9 sheets defined 73.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 4.176A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.738A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.621A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.802A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.331A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.561A pdb=" N LYS A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.002 0.041 32121 Z= 0.152 Angle : 0.553 14.730 43234 Z= 0.290 Chirality : 0.038 0.195 4593 Planarity : 0.003 0.054 5492 Dihedral : 17.355 89.403 11976 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.20 % Allowed : 26.25 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3689 helix: 1.16 (0.11), residues: 2421 sheet: -0.85 (0.55), residues: 30 loop : -0.11 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 143 HIS 0.017 0.001 HIS D 349 PHE 0.025 0.001 PHE C 744 TYR 0.025 0.001 TYR D 552 ARG 0.005 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 411 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8722 (tpp) cc_final: 0.8481 (ttm) REVERT: A 323 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8476 (mm110) REVERT: A 354 PHE cc_start: 0.8412 (t80) cc_final: 0.8009 (t80) REVERT: A 389 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8342 (tt0) REVERT: A 394 ILE cc_start: 0.8741 (mm) cc_final: 0.8491 (mm) REVERT: A 398 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7730 (pttm) REVERT: A 731 GLU cc_start: 0.8280 (tt0) cc_final: 0.7914 (tp30) REVERT: A 930 MET cc_start: 0.4432 (mmp) cc_final: 0.3393 (mtm) REVERT: B 339 HIS cc_start: 0.7958 (m170) cc_final: 0.7639 (m170) REVERT: B 341 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8145 (mm-30) REVERT: B 376 LYS cc_start: 0.8614 (tttt) cc_final: 0.8357 (ttpt) REVERT: B 518 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 624 GLU cc_start: 0.7206 (tp30) cc_final: 0.6954 (tm-30) REVERT: B 625 TYR cc_start: 0.7849 (t80) cc_final: 0.7556 (t80) REVERT: B 672 SER cc_start: 0.8735 (m) cc_final: 0.8443 (p) REVERT: B 677 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7533 (ptm-80) REVERT: B 714 SER cc_start: 0.9075 (t) cc_final: 0.8779 (p) REVERT: B 730 GLU cc_start: 0.7900 (mp0) cc_final: 0.7654 (tt0) REVERT: C 101 ASP cc_start: 0.8585 (m-30) cc_final: 0.8270 (m-30) REVERT: C 173 ASP cc_start: 0.9192 (p0) cc_final: 0.8986 (p0) REVERT: C 284 GLU cc_start: 0.8412 (tp30) cc_final: 0.8108 (tp30) REVERT: C 331 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6223 (mtpp) REVERT: C 424 PHE cc_start: 0.7440 (t80) cc_final: 0.6956 (t80) REVERT: C 616 MET cc_start: -0.1945 (mtt) cc_final: -0.2285 (mtt) REVERT: C 704 MET cc_start: 0.1236 (ppp) cc_final: 0.0986 (ppp) REVERT: C 784 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7178 (pt0) REVERT: C 866 MET cc_start: 0.4078 (mtp) cc_final: 0.3008 (tpp) REVERT: D 173 ASP cc_start: 0.9153 (p0) cc_final: 0.8943 (p0) REVERT: D 316 ILE cc_start: 0.8580 (mm) cc_final: 0.8315 (mm) REVERT: D 324 TYR cc_start: 0.5634 (t80) cc_final: 0.5384 (t80) REVERT: D 327 LYS cc_start: 0.5757 (mmtp) cc_final: 0.4797 (tptt) REVERT: D 396 MET cc_start: 0.4640 (tpt) cc_final: 0.4376 (tpt) REVERT: D 454 LEU cc_start: 0.6759 (tp) cc_final: 0.6415 (mt) REVERT: D 594 PHE cc_start: 0.8530 (t80) cc_final: 0.8307 (t80) REVERT: D 596 TYR cc_start: 0.7051 (m-80) cc_final: 0.6652 (m-80) REVERT: D 704 MET cc_start: -0.0406 (tpt) cc_final: -0.0807 (tpp) REVERT: D 709 TYR cc_start: 0.7196 (t80) cc_final: 0.6356 (t80) REVERT: D 976 MET cc_start: 0.1023 (tmm) cc_final: -0.1795 (ppp) outliers start: 7 outliers final: 2 residues processed: 416 average time/residue: 0.3720 time to fit residues: 246.3008 Evaluate side-chains 296 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain C residue 912 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 8.9990 chunk 284 optimal weight: 0.8980 chunk 157 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 351 ASN A 666 ASN ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN C 133 ASN C 349 HIS C 386 ASN C 391 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 ASN C 786 HIS C 834 GLN C 852 HIS D 339 HIS ** D 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN D 606 HIS D 786 HIS ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 939 GLN D1002 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32121 Z= 0.190 Angle : 0.559 16.369 43234 Z= 0.295 Chirality : 0.040 0.193 4593 Planarity : 0.004 0.051 5492 Dihedral : 4.093 39.318 4127 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.71 % Allowed : 23.01 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3689 helix: 1.24 (0.10), residues: 2487 sheet: -2.07 (0.73), residues: 20 loop : 0.05 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 143 HIS 0.007 0.001 HIS D 339 PHE 0.022 0.001 PHE C 544 TYR 0.026 0.001 TYR C 479 ARG 0.008 0.001 ARG C 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 332 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8723 (tpp) cc_final: 0.8430 (ttm) REVERT: A 306 ASP cc_start: 0.7770 (p0) cc_final: 0.7311 (m-30) REVERT: A 354 PHE cc_start: 0.8354 (t80) cc_final: 0.8007 (t80) REVERT: A 389 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8245 (tt0) REVERT: A 394 ILE cc_start: 0.8813 (mm) cc_final: 0.8577 (mm) REVERT: A 398 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7635 (pttm) REVERT: A 731 GLU cc_start: 0.8262 (tt0) cc_final: 0.7967 (tp30) REVERT: A 813 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7133 (mmtp) REVERT: A 930 MET cc_start: 0.4181 (mmp) cc_final: 0.2806 (mtm) REVERT: A 936 MET cc_start: 0.3882 (mtp) cc_final: 0.3483 (mmm) REVERT: A 962 TYR cc_start: 0.5529 (m-10) cc_final: 0.5319 (m-10) REVERT: B 9 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6637 (tptp) REVERT: B 191 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (mm) REVERT: B 304 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7500 (ptmt) REVERT: B 339 HIS cc_start: 0.7951 (m170) cc_final: 0.7628 (m170) REVERT: B 341 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 376 LYS cc_start: 0.8600 (tttt) cc_final: 0.8358 (ttpt) REVERT: B 518 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 624 GLU cc_start: 0.7351 (tp30) cc_final: 0.6955 (tm-30) REVERT: B 625 TYR cc_start: 0.7909 (t80) cc_final: 0.7518 (t80) REVERT: B 672 SER cc_start: 0.8830 (m) cc_final: 0.8528 (p) REVERT: B 677 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7473 (ptm-80) REVERT: B 714 SER cc_start: 0.9102 (t) cc_final: 0.8836 (p) REVERT: B 913 MET cc_start: 0.5791 (pmm) cc_final: 0.5495 (ttt) REVERT: B 930 MET cc_start: 0.5135 (mmp) cc_final: 0.3821 (ppp) REVERT: C 101 ASP cc_start: 0.8488 (m-30) cc_final: 0.8181 (m-30) REVERT: C 284 GLU cc_start: 0.8517 (tp30) cc_final: 0.8145 (tp30) REVERT: C 426 GLU cc_start: 0.7722 (pp20) cc_final: 0.6733 (mm-30) REVERT: C 449 GLU cc_start: 0.7645 (tt0) cc_final: 0.7441 (tm-30) REVERT: C 458 ILE cc_start: 0.8207 (mt) cc_final: 0.7915 (mt) REVERT: C 654 ASN cc_start: 0.5743 (OUTLIER) cc_final: 0.5519 (m-40) REVERT: C 704 MET cc_start: 0.1383 (ppp) cc_final: 0.0405 (ptt) REVERT: C 784 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7255 (pt0) REVERT: C 866 MET cc_start: 0.4476 (mtp) cc_final: 0.3480 (tpp) REVERT: D 173 ASP cc_start: 0.9197 (p0) cc_final: 0.8978 (p0) REVERT: D 324 TYR cc_start: 0.5599 (t80) cc_final: 0.5301 (t80) REVERT: D 327 LYS cc_start: 0.5555 (mmtp) cc_final: 0.4462 (tttm) REVERT: D 521 ASN cc_start: 0.6155 (t0) cc_final: 0.5940 (t0) REVERT: D 649 TYR cc_start: 0.4840 (t80) cc_final: 0.4554 (t80) REVERT: D 704 MET cc_start: -0.0450 (tpt) cc_final: -0.0752 (tpp) REVERT: D 709 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6366 (t80) REVERT: D 976 MET cc_start: 0.1816 (tmm) cc_final: -0.0914 (ppp) outliers start: 94 outliers final: 37 residues processed: 409 average time/residue: 0.4160 time to fit residues: 274.4901 Evaluate side-chains 329 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 286 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 303 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN B1002 ASN C 118 HIS C 591 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 HIS D 782 GLN D 863 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32121 Z= 0.297 Angle : 0.562 15.202 43234 Z= 0.297 Chirality : 0.041 0.189 4593 Planarity : 0.004 0.052 5492 Dihedral : 4.143 49.329 4124 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.18 % Allowed : 22.58 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3689 helix: 1.11 (0.10), residues: 2483 sheet: -2.65 (0.81), residues: 20 loop : -0.01 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 143 HIS 0.015 0.001 HIS D 339 PHE 0.027 0.002 PHE C 544 TYR 0.024 0.002 TYR D 452 ARG 0.007 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 303 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8764 (tpp) cc_final: 0.8461 (ttm) REVERT: A 306 ASP cc_start: 0.7869 (p0) cc_final: 0.7430 (m-30) REVERT: A 386 ASN cc_start: 0.8695 (m110) cc_final: 0.8374 (m-40) REVERT: A 389 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8295 (tt0) REVERT: A 398 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7779 (pttm) REVERT: A 523 ASN cc_start: 0.8907 (t0) cc_final: 0.8656 (t0) REVERT: A 677 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7470 (ttt-90) REVERT: A 731 GLU cc_start: 0.8263 (tt0) cc_final: 0.7960 (tp30) REVERT: A 743 TYR cc_start: 0.7516 (m-80) cc_final: 0.7181 (m-80) REVERT: A 755 TYR cc_start: 0.7482 (t80) cc_final: 0.7266 (t80) REVERT: A 930 MET cc_start: 0.4202 (mmp) cc_final: 0.2738 (mtt) REVERT: A 936 MET cc_start: 0.3784 (mtp) cc_final: 0.2738 (mmm) REVERT: A 970 ILE cc_start: 0.7529 (mt) cc_final: 0.7275 (tp) REVERT: B 9 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6626 (mmtp) REVERT: B 76 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8484 (mmtt) REVERT: B 134 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.6804 (p90) REVERT: B 339 HIS cc_start: 0.7938 (m170) cc_final: 0.7583 (m170) REVERT: B 341 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8170 (mm-30) REVERT: B 518 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 624 GLU cc_start: 0.7482 (tp30) cc_final: 0.7023 (tm-30) REVERT: B 672 SER cc_start: 0.8872 (m) cc_final: 0.8455 (p) REVERT: B 677 ARG cc_start: 0.7563 (ttp-170) cc_final: 0.7340 (ptm-80) REVERT: B 714 SER cc_start: 0.9073 (t) cc_final: 0.8825 (p) REVERT: B 913 MET cc_start: 0.5625 (pmm) cc_final: 0.5406 (ttt) REVERT: B 930 MET cc_start: 0.5202 (mmp) cc_final: 0.3864 (ppp) REVERT: B 976 MET cc_start: 0.4745 (OUTLIER) cc_final: 0.4395 (tmm) REVERT: C 101 ASP cc_start: 0.8526 (m-30) cc_final: 0.8264 (m-30) REVERT: C 426 GLU cc_start: 0.7934 (pp20) cc_final: 0.7051 (mm-30) REVERT: C 449 GLU cc_start: 0.7713 (tt0) cc_final: 0.7495 (tm-30) REVERT: C 527 LEU cc_start: 0.2783 (OUTLIER) cc_final: 0.2455 (tp) REVERT: C 654 ASN cc_start: 0.5764 (OUTLIER) cc_final: 0.5493 (m-40) REVERT: C 704 MET cc_start: 0.1573 (ppp) cc_final: 0.0488 (ptp) REVERT: C 784 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7224 (pt0) REVERT: C 866 MET cc_start: 0.4298 (mtp) cc_final: 0.3276 (tpp) REVERT: D 181 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: D 284 GLU cc_start: 0.8577 (tp30) cc_final: 0.8316 (tp30) REVERT: D 291 ASP cc_start: 0.8142 (p0) cc_final: 0.7239 (m-30) REVERT: D 324 TYR cc_start: 0.5684 (t80) cc_final: 0.5403 (t80) REVERT: D 327 LYS cc_start: 0.5394 (mmtp) cc_final: 0.4264 (tptt) REVERT: D 533 PHE cc_start: 0.6466 (m-10) cc_final: 0.6076 (m-80) REVERT: D 581 ASP cc_start: 0.4640 (OUTLIER) cc_final: 0.3911 (t0) REVERT: D 649 TYR cc_start: 0.4892 (t80) cc_final: 0.4594 (t80) REVERT: D 704 MET cc_start: -0.0338 (tpt) cc_final: -0.0733 (tpp) REVERT: D 709 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6446 (t80) outliers start: 110 outliers final: 58 residues processed: 395 average time/residue: 0.4118 time to fit residues: 265.4911 Evaluate side-chains 347 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 281 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32121 Z= 0.328 Angle : 0.558 16.645 43234 Z= 0.294 Chirality : 0.041 0.200 4593 Planarity : 0.004 0.065 5492 Dihedral : 4.196 52.994 4124 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.21 % Allowed : 23.59 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.13), residues: 3689 helix: 1.01 (0.10), residues: 2490 sheet: -2.87 (0.87), residues: 20 loop : -0.10 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 448 HIS 0.016 0.001 HIS D 339 PHE 0.029 0.002 PHE D 708 TYR 0.025 0.002 TYR D 552 ARG 0.008 0.001 ARG C 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 292 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 98 MET cc_start: 0.8765 (tpp) cc_final: 0.8472 (ttm) REVERT: A 306 ASP cc_start: 0.7917 (p0) cc_final: 0.7439 (m-30) REVERT: A 389 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8409 (tt0) REVERT: A 398 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7819 (pttm) REVERT: A 677 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7327 (ttt-90) REVERT: A 731 GLU cc_start: 0.8279 (tt0) cc_final: 0.7925 (tp30) REVERT: A 778 PHE cc_start: 0.8059 (t80) cc_final: 0.7694 (t80) REVERT: A 813 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7215 (mmtp) REVERT: A 930 MET cc_start: 0.4025 (mmp) cc_final: 0.2559 (mtt) REVERT: A 936 MET cc_start: 0.3592 (mtp) cc_final: 0.2567 (mmm) REVERT: B 9 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6218 (mmtp) REVERT: B 76 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8539 (mmtt) REVERT: B 134 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.6833 (p90) REVERT: B 304 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7677 (ptmt) REVERT: B 339 HIS cc_start: 0.7987 (m170) cc_final: 0.7661 (m170) REVERT: B 341 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8134 (mm-30) REVERT: B 518 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 580 SER cc_start: 0.8197 (m) cc_final: 0.7686 (t) REVERT: B 624 GLU cc_start: 0.7456 (tp30) cc_final: 0.7023 (tm-30) REVERT: B 672 SER cc_start: 0.8903 (m) cc_final: 0.8442 (p) REVERT: B 677 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7294 (ptm-80) REVERT: B 714 SER cc_start: 0.9057 (t) cc_final: 0.8800 (p) REVERT: B 913 MET cc_start: 0.5623 (pmm) cc_final: 0.5040 (ptp) REVERT: C 35 GLU cc_start: 0.8102 (tp30) cc_final: 0.7658 (tt0) REVERT: C 101 ASP cc_start: 0.8529 (m-30) cc_final: 0.8327 (m-30) REVERT: C 281 ASP cc_start: 0.7558 (t0) cc_final: 0.7283 (t0) REVERT: C 426 GLU cc_start: 0.8096 (pp20) cc_final: 0.7287 (mm-30) REVERT: C 449 GLU cc_start: 0.7809 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 654 ASN cc_start: 0.5724 (OUTLIER) cc_final: 0.5479 (m-40) REVERT: C 704 MET cc_start: 0.1612 (ppp) cc_final: 0.0557 (ptp) REVERT: C 784 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7185 (pt0) REVERT: C 866 MET cc_start: 0.4211 (mtp) cc_final: 0.3280 (tpp) REVERT: C 924 GLU cc_start: 0.2894 (OUTLIER) cc_final: 0.2661 (mp0) REVERT: D 181 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: D 284 GLU cc_start: 0.8630 (tp30) cc_final: 0.8202 (tp30) REVERT: D 324 TYR cc_start: 0.5805 (t80) cc_final: 0.5394 (t80) REVERT: D 327 LYS cc_start: 0.5574 (mmtp) cc_final: 0.4419 (tttt) REVERT: D 557 LYS cc_start: -0.2325 (OUTLIER) cc_final: -0.2787 (tmtt) REVERT: D 581 ASP cc_start: 0.4686 (OUTLIER) cc_final: 0.3896 (t0) REVERT: D 649 TYR cc_start: 0.4811 (t80) cc_final: 0.4400 (t80) REVERT: D 831 LYS cc_start: 0.3692 (OUTLIER) cc_final: 0.3459 (tppt) REVERT: D 930 MET cc_start: -0.4956 (mtp) cc_final: -0.5288 (mtp) outliers start: 111 outliers final: 66 residues processed: 386 average time/residue: 0.4257 time to fit residues: 268.4300 Evaluate side-chains 350 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 273 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 813 LYS Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 831 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 309 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 609 HIS ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 HIS B 832 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32121 Z= 0.200 Angle : 0.515 16.638 43234 Z= 0.270 Chirality : 0.039 0.212 4593 Planarity : 0.003 0.065 5492 Dihedral : 4.109 54.399 4124 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.00 % Allowed : 23.79 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3689 helix: 1.12 (0.10), residues: 2476 sheet: -3.23 (0.89), residues: 20 loop : 0.02 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 448 HIS 0.010 0.001 HIS C 979 PHE 0.026 0.001 PHE D 708 TYR 0.027 0.001 TYR D 552 ARG 0.005 0.000 ARG D 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 303 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.9031 (t80) cc_final: 0.8747 (t80) REVERT: A 98 MET cc_start: 0.8764 (tpp) cc_final: 0.8443 (ttm) REVERT: A 306 ASP cc_start: 0.7863 (p0) cc_final: 0.7297 (m-30) REVERT: A 389 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8393 (tt0) REVERT: A 398 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7871 (pttm) REVERT: A 447 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7715 (ptm160) REVERT: A 627 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6661 (ttp-110) REVERT: A 677 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7323 (ttt-90) REVERT: A 731 GLU cc_start: 0.8258 (tt0) cc_final: 0.7898 (tp30) REVERT: A 743 TYR cc_start: 0.7612 (m-80) cc_final: 0.7259 (m-80) REVERT: A 778 PHE cc_start: 0.8122 (t80) cc_final: 0.7747 (t80) REVERT: A 813 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7304 (mmtp) REVERT: A 930 MET cc_start: 0.3999 (mmp) cc_final: 0.2489 (mtt) REVERT: A 936 MET cc_start: 0.3871 (mtp) cc_final: 0.2760 (mmm) REVERT: B 9 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6442 (mmtt) REVERT: B 76 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8520 (mmtt) REVERT: B 134 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.6778 (p90) REVERT: B 304 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: B 339 HIS cc_start: 0.7959 (m170) cc_final: 0.7637 (m170) REVERT: B 341 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8086 (mm-30) REVERT: B 518 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8228 (mt-10) REVERT: B 624 GLU cc_start: 0.7432 (tp30) cc_final: 0.7027 (tm-30) REVERT: B 672 SER cc_start: 0.8912 (m) cc_final: 0.8461 (p) REVERT: B 677 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.7308 (ptm-80) REVERT: B 714 SER cc_start: 0.9057 (t) cc_final: 0.8807 (p) REVERT: B 784 GLU cc_start: 0.8775 (mm-30) cc_final: 0.7984 (tm-30) REVERT: B 913 MET cc_start: 0.5703 (pmm) cc_final: 0.5152 (ptp) REVERT: B 930 MET cc_start: 0.5256 (mmp) cc_final: 0.3982 (ppp) REVERT: B 976 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.4601 (tmm) REVERT: C 35 GLU cc_start: 0.8096 (tp30) cc_final: 0.7704 (tt0) REVERT: C 101 ASP cc_start: 0.8538 (m-30) cc_final: 0.8283 (m-30) REVERT: C 382 ASN cc_start: 0.8143 (m110) cc_final: 0.7822 (p0) REVERT: C 426 GLU cc_start: 0.8128 (pp20) cc_final: 0.7329 (mm-30) REVERT: C 654 ASN cc_start: 0.5756 (OUTLIER) cc_final: 0.5436 (m-40) REVERT: C 704 MET cc_start: 0.1620 (ppp) cc_final: 0.0740 (ptp) REVERT: C 784 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7172 (pt0) REVERT: C 866 MET cc_start: 0.4189 (mtp) cc_final: 0.3241 (tpp) REVERT: C 924 GLU cc_start: 0.2974 (OUTLIER) cc_final: 0.2762 (mp0) REVERT: D 284 GLU cc_start: 0.8504 (tp30) cc_final: 0.8250 (tp30) REVERT: D 324 TYR cc_start: 0.5767 (t80) cc_final: 0.5369 (t80) REVERT: D 327 LYS cc_start: 0.5374 (mmtp) cc_final: 0.4248 (tttt) REVERT: D 391 ASN cc_start: 0.6346 (m-40) cc_final: 0.5517 (m110) REVERT: D 477 ASN cc_start: 0.8180 (m110) cc_final: 0.7507 (m-40) REVERT: D 557 LYS cc_start: -0.2415 (OUTLIER) cc_final: -0.3125 (ttpp) REVERT: D 581 ASP cc_start: 0.4734 (OUTLIER) cc_final: 0.3912 (t0) REVERT: D 649 TYR cc_start: 0.4595 (t80) cc_final: 0.4024 (t80) REVERT: D 930 MET cc_start: -0.4898 (mtp) cc_final: -0.5241 (mtp) outliers start: 104 outliers final: 59 residues processed: 386 average time/residue: 0.4174 time to fit residues: 260.9034 Evaluate side-chains 343 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 274 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 581 ASP Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.0670 chunk 326 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 212 optimal weight: 0.0570 chunk 89 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** D 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN ** D 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 32121 Z= 0.161 Angle : 0.506 15.930 43234 Z= 0.266 Chirality : 0.038 0.187 4593 Planarity : 0.003 0.069 5492 Dihedral : 4.030 54.304 4124 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.63 % Allowed : 24.29 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3689 helix: 1.22 (0.10), residues: 2484 sheet: -2.92 (0.73), residues: 32 loop : 0.07 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 448 HIS 0.012 0.001 HIS D 339 PHE 0.030 0.001 PHE C 544 TYR 0.027 0.001 TYR D 552 ARG 0.008 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 300 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.9004 (t80) cc_final: 0.8709 (t80) REVERT: A 98 MET cc_start: 0.8783 (tpp) cc_final: 0.8429 (ttm) REVERT: A 389 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8346 (tt0) REVERT: A 398 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7864 (pttm) REVERT: A 447 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7761 (ptm160) REVERT: A 627 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6751 (ttp-110) REVERT: A 677 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7247 (ttt-90) REVERT: A 731 GLU cc_start: 0.8271 (tt0) cc_final: 0.7903 (tp30) REVERT: A 743 TYR cc_start: 0.7525 (m-80) cc_final: 0.7133 (m-80) REVERT: A 755 TYR cc_start: 0.7615 (t80) cc_final: 0.7344 (t80) REVERT: A 778 PHE cc_start: 0.8094 (t80) cc_final: 0.7731 (t80) REVERT: A 813 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7285 (mmtp) REVERT: A 930 MET cc_start: 0.3984 (mmp) cc_final: 0.2433 (mtt) REVERT: A 936 MET cc_start: 0.3965 (mtp) cc_final: 0.2817 (mmm) REVERT: A 970 ILE cc_start: 0.7733 (mt) cc_final: 0.7517 (mm) REVERT: B 9 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6483 (mmtt) REVERT: B 76 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8485 (mmtt) REVERT: B 134 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.6716 (p90) REVERT: B 304 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7664 (ptmt) REVERT: B 339 HIS cc_start: 0.7936 (m170) cc_final: 0.7633 (m170) REVERT: B 341 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 518 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 624 GLU cc_start: 0.7416 (tp30) cc_final: 0.7017 (tm-30) REVERT: B 672 SER cc_start: 0.8930 (m) cc_final: 0.8509 (p) REVERT: B 677 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7390 (ptm-80) REVERT: B 714 SER cc_start: 0.9088 (t) cc_final: 0.8845 (p) REVERT: B 731 GLU cc_start: 0.8414 (pm20) cc_final: 0.8201 (pm20) REVERT: B 759 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8209 (tt0) REVERT: B 784 GLU cc_start: 0.8751 (mm-30) cc_final: 0.7996 (tm-30) REVERT: B 930 MET cc_start: 0.5267 (mmp) cc_final: 0.3989 (ppp) REVERT: B 976 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.4590 (tmm) REVERT: C 35 GLU cc_start: 0.8073 (tp30) cc_final: 0.7707 (tt0) REVERT: C 101 ASP cc_start: 0.8406 (m-30) cc_final: 0.8140 (m-30) REVERT: C 281 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6823 (t0) REVERT: C 396 MET cc_start: 0.5701 (mmm) cc_final: 0.5462 (mmm) REVERT: C 426 GLU cc_start: 0.8152 (pp20) cc_final: 0.7377 (mm-30) REVERT: C 704 MET cc_start: 0.1574 (ppp) cc_final: 0.0771 (ptp) REVERT: C 784 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7254 (pt0) REVERT: C 866 MET cc_start: 0.4182 (mtp) cc_final: 0.3279 (tpp) REVERT: C 924 GLU cc_start: 0.2991 (OUTLIER) cc_final: 0.2778 (mp0) REVERT: D 284 GLU cc_start: 0.8553 (tp30) cc_final: 0.8294 (tp30) REVERT: D 311 TYR cc_start: 0.6708 (t80) cc_final: 0.6441 (t80) REVERT: D 324 TYR cc_start: 0.5756 (t80) cc_final: 0.5384 (t80) REVERT: D 327 LYS cc_start: 0.5305 (mmtp) cc_final: 0.4172 (tttt) REVERT: D 361 PHE cc_start: 0.4845 (m-10) cc_final: 0.4368 (m-10) REVERT: D 391 ASN cc_start: 0.6350 (m-40) cc_final: 0.5500 (m110) REVERT: D 540 LYS cc_start: 0.8238 (tptm) cc_final: 0.7948 (tptp) REVERT: D 709 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6340 (t80) REVERT: D 930 MET cc_start: -0.4926 (mtp) cc_final: -0.5236 (mtp) REVERT: D 976 MET cc_start: 0.1870 (tmm) cc_final: -0.1028 (ptt) outliers start: 91 outliers final: 58 residues processed: 371 average time/residue: 0.4203 time to fit residues: 251.9473 Evaluate side-chains 346 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 279 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 611 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 912 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 361 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32121 Z= 0.186 Angle : 0.516 15.543 43234 Z= 0.269 Chirality : 0.039 0.182 4593 Planarity : 0.003 0.051 5492 Dihedral : 4.013 55.241 4124 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.69 % Allowed : 24.17 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3689 helix: 1.25 (0.10), residues: 2482 sheet: -2.98 (0.75), residues: 32 loop : 0.07 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 448 HIS 0.010 0.001 HIS D 339 PHE 0.025 0.001 PHE D 708 TYR 0.039 0.001 TYR D 649 ARG 0.014 0.000 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 295 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8808 (tpp) cc_final: 0.8443 (ttm) REVERT: A 389 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8347 (tt0) REVERT: A 398 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7882 (pttm) REVERT: A 447 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7816 (ptm160) REVERT: A 677 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7236 (ttt-90) REVERT: A 731 GLU cc_start: 0.8272 (tt0) cc_final: 0.7902 (tp30) REVERT: A 743 TYR cc_start: 0.7512 (m-80) cc_final: 0.7073 (m-80) REVERT: A 755 TYR cc_start: 0.7695 (t80) cc_final: 0.7439 (t80) REVERT: A 778 PHE cc_start: 0.8184 (t80) cc_final: 0.7829 (t80) REVERT: A 813 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7284 (mmtp) REVERT: A 930 MET cc_start: 0.3998 (mmp) cc_final: 0.2434 (mtt) REVERT: A 936 MET cc_start: 0.3979 (mtp) cc_final: 0.2839 (mmm) REVERT: B 9 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6403 (mmtt) REVERT: B 76 LYS cc_start: 0.8711 (mmtp) cc_final: 0.8480 (mmtt) REVERT: B 134 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.6731 (p90) REVERT: B 304 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7672 (ptmt) REVERT: B 339 HIS cc_start: 0.7923 (m170) cc_final: 0.7617 (m170) REVERT: B 341 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 518 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 624 GLU cc_start: 0.7450 (tp30) cc_final: 0.7028 (tm-30) REVERT: B 672 SER cc_start: 0.8906 (m) cc_final: 0.8467 (p) REVERT: B 677 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7418 (ptm-80) REVERT: B 714 SER cc_start: 0.9072 (t) cc_final: 0.8838 (p) REVERT: B 784 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8011 (tm-30) REVERT: B 1004 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.4953 (m-80) REVERT: C 35 GLU cc_start: 0.8086 (tp30) cc_final: 0.7720 (tt0) REVERT: C 101 ASP cc_start: 0.8425 (m-30) cc_final: 0.8153 (m-30) REVERT: C 281 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6803 (t0) REVERT: C 426 GLU cc_start: 0.8158 (pp20) cc_final: 0.7419 (mm-30) REVERT: C 441 PHE cc_start: 0.8168 (m-10) cc_final: 0.7599 (m-80) REVERT: C 654 ASN cc_start: 0.5590 (OUTLIER) cc_final: 0.5210 (m-40) REVERT: C 704 MET cc_start: 0.1604 (ppp) cc_final: 0.0778 (ptp) REVERT: C 784 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7240 (pt0) REVERT: C 866 MET cc_start: 0.4177 (mtp) cc_final: 0.3243 (tpp) REVERT: C 924 GLU cc_start: 0.3022 (OUTLIER) cc_final: 0.2800 (mp0) REVERT: D 284 GLU cc_start: 0.8590 (tp30) cc_final: 0.8313 (tp30) REVERT: D 311 TYR cc_start: 0.6781 (t80) cc_final: 0.6507 (t80) REVERT: D 324 TYR cc_start: 0.5799 (t80) cc_final: 0.5422 (t80) REVERT: D 327 LYS cc_start: 0.5350 (mmtp) cc_final: 0.4115 (tttt) REVERT: D 362 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.5145 (tp30) REVERT: D 391 ASN cc_start: 0.6299 (m-40) cc_final: 0.5418 (m110) REVERT: D 540 LYS cc_start: 0.8330 (tptm) cc_final: 0.8073 (tptp) REVERT: D 649 TYR cc_start: 0.4536 (t80) cc_final: 0.4231 (t80) REVERT: D 709 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6370 (t80) REVERT: D 930 MET cc_start: -0.4979 (mtp) cc_final: -0.5277 (mtp) outliers start: 93 outliers final: 65 residues processed: 372 average time/residue: 0.4567 time to fit residues: 279.0834 Evaluate side-chains 352 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 276 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 654 ASN Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 332 HIS ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32121 Z= 0.305 Angle : 0.556 15.096 43234 Z= 0.290 Chirality : 0.040 0.202 4593 Planarity : 0.004 0.073 5492 Dihedral : 4.026 20.969 4122 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.89 % Allowed : 24.20 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3689 helix: 1.13 (0.10), residues: 2485 sheet: -3.57 (0.91), residues: 20 loop : -0.03 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 448 HIS 0.018 0.001 HIS D 339 PHE 0.029 0.002 PHE A1004 TYR 0.026 0.002 TYR D 649 ARG 0.010 0.001 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 279 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 98 MET cc_start: 0.8814 (tpp) cc_final: 0.8460 (ttm) REVERT: A 389 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8400 (tt0) REVERT: A 447 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7788 (ptm160) REVERT: A 627 ARG cc_start: 0.7066 (ttp-110) cc_final: 0.6468 (ptm-80) REVERT: A 677 ARG cc_start: 0.7942 (ptt90) cc_final: 0.7281 (ttt-90) REVERT: A 731 GLU cc_start: 0.8324 (tt0) cc_final: 0.7904 (tp30) REVERT: A 743 TYR cc_start: 0.7575 (m-80) cc_final: 0.7125 (m-80) REVERT: A 813 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7361 (mmtp) REVERT: A 930 MET cc_start: 0.4090 (mmp) cc_final: 0.2502 (mtt) REVERT: A 936 MET cc_start: 0.3950 (mtp) cc_final: 0.2782 (mmm) REVERT: B 9 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6203 (mmtt) REVERT: B 76 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8553 (mmtt) REVERT: B 134 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.6861 (p90) REVERT: B 295 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 304 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7679 (ptmt) REVERT: B 331 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7910 (mtpt) REVERT: B 339 HIS cc_start: 0.7946 (m170) cc_final: 0.7716 (m170) REVERT: B 341 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 518 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 580 SER cc_start: 0.8194 (m) cc_final: 0.7684 (t) REVERT: B 624 GLU cc_start: 0.7487 (tp30) cc_final: 0.7062 (tm-30) REVERT: B 672 SER cc_start: 0.8872 (m) cc_final: 0.8409 (p) REVERT: B 677 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7386 (ptm-80) REVERT: B 714 SER cc_start: 0.9036 (t) cc_final: 0.8798 (p) REVERT: B 730 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 759 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8202 (tt0) REVERT: B 784 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7879 (tm-30) REVERT: B 936 MET cc_start: 0.2781 (pmm) cc_final: 0.2261 (pmm) REVERT: B 1004 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.5021 (m-80) REVERT: C 35 GLU cc_start: 0.8120 (tp30) cc_final: 0.7747 (tt0) REVERT: C 69 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: C 396 MET cc_start: 0.5026 (mmm) cc_final: 0.4716 (mmm) REVERT: C 426 GLU cc_start: 0.8217 (pp20) cc_final: 0.7441 (mm-30) REVERT: C 704 MET cc_start: 0.1509 (ppp) cc_final: 0.0752 (ptp) REVERT: C 866 MET cc_start: 0.4206 (mtp) cc_final: 0.3315 (tpp) REVERT: C 924 GLU cc_start: 0.2994 (OUTLIER) cc_final: 0.2779 (mp0) REVERT: D 284 GLU cc_start: 0.8633 (tp30) cc_final: 0.8357 (tp30) REVERT: D 324 TYR cc_start: 0.5746 (t80) cc_final: 0.5350 (t80) REVERT: D 327 LYS cc_start: 0.5360 (mmtp) cc_final: 0.4113 (tttt) REVERT: D 362 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.5094 (tp30) REVERT: D 540 LYS cc_start: 0.8450 (tptm) cc_final: 0.8204 (tptp) REVERT: D 709 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6395 (t80) REVERT: D 930 MET cc_start: -0.4964 (mtp) cc_final: -0.5220 (mtp) outliers start: 100 outliers final: 67 residues processed: 362 average time/residue: 0.4192 time to fit residues: 245.2933 Evaluate side-chains 345 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 264 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 814 ASN Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Chi-restraints excluded: chain D residue 975 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 3.9990 chunk 346 optimal weight: 0.1980 chunk 315 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 304 optimal weight: 0.2980 chunk 318 optimal weight: 0.9990 chunk 335 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 HIS ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32121 Z= 0.167 Angle : 0.519 13.869 43234 Z= 0.270 Chirality : 0.039 0.198 4593 Planarity : 0.003 0.062 5492 Dihedral : 3.931 20.220 4122 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 25.06 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3689 helix: 1.22 (0.10), residues: 2484 sheet: -3.64 (0.91), residues: 20 loop : 0.04 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 143 HIS 0.010 0.001 HIS D 339 PHE 0.036 0.001 PHE D 528 TYR 0.042 0.001 TYR D 649 ARG 0.008 0.000 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 284 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.9038 (t80) cc_final: 0.8759 (t80) REVERT: A 98 MET cc_start: 0.8802 (tpp) cc_final: 0.8450 (ttm) REVERT: A 339 HIS cc_start: 0.7751 (m90) cc_final: 0.7515 (m90) REVERT: A 389 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8362 (tt0) REVERT: A 447 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7817 (ptm160) REVERT: A 677 ARG cc_start: 0.7937 (ptt90) cc_final: 0.7259 (ttt-90) REVERT: A 731 GLU cc_start: 0.8322 (tt0) cc_final: 0.7856 (tp30) REVERT: A 743 TYR cc_start: 0.7524 (m-80) cc_final: 0.7033 (m-80) REVERT: A 755 TYR cc_start: 0.7770 (t80) cc_final: 0.7438 (t80) REVERT: A 813 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7325 (mmtp) REVERT: A 930 MET cc_start: 0.4032 (mmp) cc_final: 0.2434 (mtt) REVERT: A 936 MET cc_start: 0.4030 (mtp) cc_final: 0.3320 (mmm) REVERT: A 979 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7358 (p90) REVERT: B 9 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6369 (mmtt) REVERT: B 76 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8489 (mmtt) REVERT: B 134 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.6789 (p90) REVERT: B 295 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: B 304 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7639 (ptmt) REVERT: B 339 HIS cc_start: 0.7927 (m170) cc_final: 0.7632 (m170) REVERT: B 341 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 428 GLN cc_start: 0.8257 (tp40) cc_final: 0.7900 (tm-30) REVERT: B 518 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 624 GLU cc_start: 0.7460 (tp30) cc_final: 0.7068 (tm-30) REVERT: B 672 SER cc_start: 0.8866 (m) cc_final: 0.8420 (p) REVERT: B 677 ARG cc_start: 0.7620 (ttp-170) cc_final: 0.7381 (ptm-80) REVERT: B 714 SER cc_start: 0.9072 (t) cc_final: 0.8841 (p) REVERT: B 759 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8200 (tt0) REVERT: B 784 GLU cc_start: 0.8740 (mm-30) cc_final: 0.7907 (tm-30) REVERT: B 936 MET cc_start: 0.2636 (pmm) cc_final: 0.2308 (pmm) REVERT: B 1004 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: C 35 GLU cc_start: 0.8081 (tp30) cc_final: 0.7712 (tt0) REVERT: C 69 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: C 101 ASP cc_start: 0.8316 (m-30) cc_final: 0.8060 (m-30) REVERT: C 281 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6785 (t0) REVERT: C 302 ILE cc_start: 0.4255 (mp) cc_final: 0.4052 (mp) REVERT: C 304 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6674 (pttp) REVERT: C 396 MET cc_start: 0.5150 (mmm) cc_final: 0.4734 (mmm) REVERT: C 426 GLU cc_start: 0.8211 (pp20) cc_final: 0.7440 (mm-30) REVERT: C 704 MET cc_start: 0.1499 (ppp) cc_final: 0.0743 (ptp) REVERT: C 784 GLU cc_start: 0.7951 (tp30) cc_final: 0.7492 (pt0) REVERT: C 866 MET cc_start: 0.4163 (mtp) cc_final: 0.3273 (tpp) REVERT: C 924 GLU cc_start: 0.3094 (OUTLIER) cc_final: 0.2868 (mp0) REVERT: D 284 GLU cc_start: 0.8588 (tp30) cc_final: 0.8322 (tp30) REVERT: D 324 TYR cc_start: 0.5725 (t80) cc_final: 0.5337 (t80) REVERT: D 327 LYS cc_start: 0.5352 (mmtp) cc_final: 0.4121 (tttt) REVERT: D 362 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.5367 (tp30) REVERT: D 388 PHE cc_start: 0.8200 (m-80) cc_final: 0.7952 (m-10) REVERT: D 391 ASN cc_start: 0.6388 (m-40) cc_final: 0.5463 (m110) REVERT: D 540 LYS cc_start: 0.8437 (tptm) cc_final: 0.8188 (tptp) REVERT: D 709 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6502 (t80) REVERT: D 930 MET cc_start: -0.4989 (mtp) cc_final: -0.5235 (mtp) outliers start: 79 outliers final: 54 residues processed: 350 average time/residue: 0.4258 time to fit residues: 243.8645 Evaluate side-chains 344 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 276 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 979 HIS Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 2.9990 chunk 356 optimal weight: 8.9990 chunk 217 optimal weight: 0.0980 chunk 168 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 373 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 229 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32121 Z= 0.317 Angle : 0.572 14.024 43234 Z= 0.297 Chirality : 0.041 0.251 4593 Planarity : 0.004 0.061 5492 Dihedral : 4.034 21.522 4122 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 25.09 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3689 helix: 1.09 (0.10), residues: 2484 sheet: -3.68 (0.93), residues: 20 loop : -0.05 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 143 HIS 0.018 0.001 HIS A 979 PHE 0.028 0.002 PHE C 708 TYR 0.027 0.002 TYR D 452 ARG 0.009 0.001 ARG C 587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7378 Ramachandran restraints generated. 3689 Oldfield, 0 Emsley, 3689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 274 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 98 MET cc_start: 0.8827 (tpp) cc_final: 0.8475 (ttm) REVERT: A 339 HIS cc_start: 0.7751 (m90) cc_final: 0.7513 (m90) REVERT: A 389 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8394 (tt0) REVERT: A 447 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7745 (ptm160) REVERT: A 731 GLU cc_start: 0.8297 (tt0) cc_final: 0.7831 (tp30) REVERT: A 743 TYR cc_start: 0.7574 (m-80) cc_final: 0.7122 (m-80) REVERT: A 813 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7387 (mmtp) REVERT: A 930 MET cc_start: 0.4137 (mmp) cc_final: 0.2483 (mtt) REVERT: A 936 MET cc_start: 0.3915 (mtp) cc_final: 0.3192 (mmm) REVERT: B 9 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6119 (mmtt) REVERT: B 76 LYS cc_start: 0.8780 (mmtp) cc_final: 0.8542 (mmtt) REVERT: B 134 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.6924 (p90) REVERT: B 304 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (ptmt) REVERT: B 339 HIS cc_start: 0.7940 (m170) cc_final: 0.7621 (m170) REVERT: B 341 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 428 GLN cc_start: 0.8266 (tp40) cc_final: 0.7876 (tm-30) REVERT: B 518 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 580 SER cc_start: 0.8204 (m) cc_final: 0.7701 (t) REVERT: B 624 GLU cc_start: 0.7481 (tp30) cc_final: 0.7052 (tm-30) REVERT: B 672 SER cc_start: 0.8922 (m) cc_final: 0.8440 (p) REVERT: B 677 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.7323 (ptm-80) REVERT: B 714 SER cc_start: 0.9049 (t) cc_final: 0.8820 (p) REVERT: B 759 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8214 (tt0) REVERT: B 784 GLU cc_start: 0.8740 (mm-30) cc_final: 0.7922 (tm-30) REVERT: B 936 MET cc_start: 0.2449 (pmm) cc_final: 0.1950 (pmm) REVERT: B 1004 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5017 (m-80) REVERT: C 35 GLU cc_start: 0.8135 (tp30) cc_final: 0.7761 (tt0) REVERT: C 69 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 101 ASP cc_start: 0.8353 (m-30) cc_final: 0.8105 (m-30) REVERT: C 281 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6854 (t0) REVERT: C 304 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6714 (pttt) REVERT: C 426 GLU cc_start: 0.8224 (pp20) cc_final: 0.7467 (mm-30) REVERT: C 704 MET cc_start: 0.1451 (ppp) cc_final: 0.0697 (ptt) REVERT: C 784 GLU cc_start: 0.7946 (tp30) cc_final: 0.7516 (pt0) REVERT: C 866 MET cc_start: 0.4215 (mtp) cc_final: 0.3316 (tpp) REVERT: C 924 GLU cc_start: 0.3099 (OUTLIER) cc_final: 0.2876 (mp0) REVERT: D 284 GLU cc_start: 0.8632 (tp30) cc_final: 0.8355 (tp30) REVERT: D 324 TYR cc_start: 0.5742 (t80) cc_final: 0.5184 (t80) REVERT: D 361 PHE cc_start: 0.4772 (m-10) cc_final: 0.4512 (m-10) REVERT: D 362 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.5150 (tp30) REVERT: D 467 ASN cc_start: 0.6538 (p0) cc_final: 0.6123 (p0) REVERT: D 709 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6547 (t80) REVERT: D 930 MET cc_start: -0.5011 (mtp) cc_final: -0.5236 (mtp) outliers start: 79 outliers final: 59 residues processed: 343 average time/residue: 0.4292 time to fit residues: 240.4961 Evaluate side-chains 332 residues out of total 3463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 260 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 560 GLU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1004 PHE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 662 ASP Chi-restraints excluded: chain C residue 709 TYR Chi-restraints excluded: chain C residue 859 VAL Chi-restraints excluded: chain C residue 897 ILE Chi-restraints excluded: chain C residue 924 GLU Chi-restraints excluded: chain C residue 975 HIS Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 LYS Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain D residue 709 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 8.9990 chunk 316 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 305 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.183665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112265 restraints weight = 51528.620| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.60 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32121 Z= 0.200 Angle : 0.542 14.699 43234 Z= 0.280 Chirality : 0.039 0.267 4593 Planarity : 0.003 0.049 5492 Dihedral : 3.966 20.639 4122 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.05 % Allowed : 25.32 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3689 helix: 1.18 (0.10), residues: 2477 sheet: -3.69 (0.92), residues: 20 loop : 0.00 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 143 HIS 0.010 0.001 HIS D 339 PHE 0.029 0.001 PHE D 708 TYR 0.028 0.001 TYR D 452 ARG 0.011 0.000 ARG C 587 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7524.94 seconds wall clock time: 228 minutes 1.29 seconds (13681.29 seconds total)