Starting phenix.real_space_refine on Fri Jul 3 09:08:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2026/7zkq_14765.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.102 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 52 5.16 5 C 8063 2.51 5 N 1987 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12352 Number of models: 1 Model: "" Number of chains: 8 Chain: "2" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3609 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 502 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain breaks: 1 Chain: "C" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3396 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 13, 'TRANS': 402} Chain: "T" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'CDL': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.64, per 1000 atoms: 0.21 Number of scatterers: 12352 At special positions: 0 Unit cell: (112.271, 140.036, 132.793, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 5 15.00 O 2245 8.00 N 1987 7.00 C 8063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 392.3 milliseconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 6 sheets defined 63.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain '2' and resid 1 through 15 removed outlier: 3.728A pdb=" N ALA 2 5 " --> pdb=" O FME 2 1 " (cutoff:3.500A) Processing helix chain '2' and resid 22 through 47 Processing helix chain '2' and resid 62 through 85 Processing helix chain '2' and resid 90 through 97 removed outlier: 3.861A pdb=" N PHE 2 97 " --> pdb=" O TYR 2 93 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 119 Processing helix chain '2' and resid 122 through 144 removed outlier: 3.839A pdb=" N TYR 2 144 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 175 removed outlier: 3.767A pdb=" N SER 2 151 " --> pdb=" O SER 2 147 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR 2 175 " --> pdb=" O SER 2 171 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 3.920A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 213 No H-bonds generated for 'chain '2' and resid 212 through 213' Processing helix chain '2' and resid 214 through 217 Processing helix chain '2' and resid 218 through 227 Processing helix chain '2' and resid 229 through 237 removed outlier: 4.673A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 238 through 251 Processing helix chain '2' and resid 257 through 274 Processing helix chain '2' and resid 275 through 278 removed outlier: 3.560A pdb=" N GLN 2 278 " --> pdb=" O GLY 2 275 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 275 through 278' Processing helix chain '2' and resid 280 through 298 Processing helix chain '2' and resid 299 through 302 Processing helix chain '2' and resid 305 through 330 Processing helix chain '2' and resid 331 through 334 removed outlier: 3.735A pdb=" N ILE 2 334 " --> pdb=" O ILE 2 331 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 331 through 334' Processing helix chain '2' and resid 346 through 351 Processing helix chain '2' and resid 352 through 356 Processing helix chain '2' and resid 357 through 373 Processing helix chain '2' and resid 377 through 392 Processing helix chain '2' and resid 396 through 421 removed outlier: 3.683A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) Processing helix chain '2' and resid 436 through 453 Processing helix chain '2' and resid 456 through 467 Processing helix chain 'b' and resid 3 through 25 Processing helix chain 'b' and resid 32 through 67 removed outlier: 3.945A pdb=" N TYR b 36 " --> pdb=" O TYR b 32 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL b 37 " --> pdb=" O PRO b 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.694A pdb=" N VAL A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'C' and resid 430 through 444 Processing helix chain 'C' and resid 446 through 460 Processing helix chain 'C' and resid 467 through 483 removed outlier: 3.848A pdb=" N GLU C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.559A pdb=" N GLY C 506 " --> pdb=" O CYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.712A pdb=" N ALA C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 removed outlier: 3.655A pdb=" N GLN C 537 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 567 removed outlier: 4.193A pdb=" N TYR C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS C 567 " --> pdb=" O TYR C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 586 Processing helix chain 'C' and resid 589 through 603 removed outlier: 4.032A pdb=" N TYR C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 630 through 645 removed outlier: 3.571A pdb=" N VAL C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 660 removed outlier: 3.670A pdb=" N LEU C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 680 Processing helix chain 'C' and resid 682 through 695 removed outlier: 3.591A pdb=" N VAL C 686 " --> pdb=" O ASP C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 714 Processing helix chain 'C' and resid 717 through 727 Processing helix chain 'C' and resid 728 through 732 Processing helix chain 'C' and resid 736 through 749 Processing helix chain 'C' and resid 752 through 768 removed outlier: 4.745A pdb=" N GLU C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 Processing helix chain 'C' and resid 785 through 800 Processing helix chain 'C' and resid 800 through 810 removed outlier: 3.557A pdb=" N GLY C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 844 removed outlier: 3.738A pdb=" N ALA C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY C 844 " --> pdb=" O GLU C 840 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 18 Processing helix chain 'T' and resid 21 through 46 Processing helix chain 'T' and resid 52 through 67 removed outlier: 3.617A pdb=" N LEU T 56 " --> pdb=" O GLY T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 86 removed outlier: 3.585A pdb=" N VAL T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP T 86 " --> pdb=" O ASP T 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 80 through 86' Processing helix chain 'T' and resid 91 through 96 removed outlier: 3.806A pdb=" N ILE T 96 " --> pdb=" O ASP T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 100 Processing helix chain 'T' and resid 120 through 124 Processing helix chain 'T' and resid 138 through 149 Processing helix chain 'T' and resid 204 through 213 removed outlier: 4.503A pdb=" N SER T 208 " --> pdb=" O ARG T 204 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 231 Processing helix chain 'T' and resid 261 through 279 removed outlier: 3.594A pdb=" N VAL T 265 " --> pdb=" O SER T 261 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU T 279 " --> pdb=" O LEU T 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 289 through 294 Processing helix chain 'T' and resid 295 through 318 removed outlier: 3.647A pdb=" N LEU T 318 " --> pdb=" O GLU T 314 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 337 removed outlier: 3.833A pdb=" N LYS T 331 " --> pdb=" O PRO T 328 " (cutoff:3.500A) Proline residue: T 333 - end of helix Processing helix chain 'T' and resid 348 through 352 Processing sheet with id=AA1, first strand: chain '2' and resid 52 through 54 removed outlier: 3.885A pdb=" N LEU 2 59 " --> pdb=" O VAL 2 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.654A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 20 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N GLU A 193 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 63 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 43 " --> pdb=" O ASN A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.654A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 20 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N GLU A 193 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A 109 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 195 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A 107 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 197 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS A 105 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 34 removed outlier: 5.491A pdb=" N VAL A 176 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 117 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'T' and resid 48 through 51 removed outlier: 6.895A pdb=" N LEU T 71 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET T 223 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL T 73 " --> pdb=" O MET T 223 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER T 225 " --> pdb=" O VAL T 73 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU T 70 " --> pdb=" O VAL T 181 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE T 183 " --> pdb=" O LEU T 70 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR T 72 " --> pdb=" O PHE T 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 346 through 347 710 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1936 1.31 - 1.44: 3418 1.44 - 1.56: 7167 1.56 - 1.68: 24 1.68 - 1.81: 93 Bond restraints: 12638 Sorted by residual: bond pdb=" C1 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.403 1.494 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CBS LMN C 901 " pdb=" CCM LMN C 901 " ideal model delta sigma weight residual 1.529 1.620 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CBJ LMN C 901 " pdb=" CBL LMN C 901 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.413 1.495 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CCF LMN C 901 " pdb=" OBX LMN C 901 " ideal model delta sigma weight residual 1.410 1.491 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 12633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 16759 1.98 - 3.96: 304 3.96 - 5.94: 51 5.94 - 7.92: 4 7.92 - 9.90: 4 Bond angle restraints: 17122 Sorted by residual: angle pdb=" N ILE 2 232 " pdb=" CA ILE 2 232 " pdb=" C ILE 2 232 " ideal model delta sigma weight residual 111.81 107.90 3.91 8.60e-01 1.35e+00 2.07e+01 angle pdb=" CA PHE A 154 " pdb=" C PHE A 154 " pdb=" O PHE A 154 " ideal model delta sigma weight residual 121.47 116.74 4.73 1.15e+00 7.56e-01 1.69e+01 angle pdb=" C GLY T 105 " pdb=" N ALA T 106 " pdb=" CA ALA T 106 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ALA A 3 " pdb=" N ASN A 4 " pdb=" CA ASN A 4 " ideal model delta sigma weight residual 120.09 124.85 -4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N ILE A 151 " pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 112.50 107.39 5.11 1.39e+00 5.18e-01 1.35e+01 ... (remaining 17117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.27: 7148 27.27 - 54.54: 308 54.54 - 81.81: 33 81.81 - 109.08: 1 109.08 - 136.35: 2 Dihedral angle restraints: 7492 sinusoidal: 3082 harmonic: 4410 Sorted by residual: dihedral pdb=" C1B PLC T 401 " pdb=" CB PLC T 401 " pdb=" O3 PLC T 401 " pdb=" C3 PLC T 401 " ideal model delta sinusoidal sigma weight residual -178.77 -42.42 -136.35 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CBG LMN C 901 " pdb=" CBI LMN C 901 " pdb=" CBK LMN C 901 " pdb=" CBQ LMN C 901 " ideal model delta sinusoidal sigma weight residual 181.33 67.02 114.31 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CA LEU 2 301 " pdb=" C LEU 2 301 " pdb=" N LEU 2 302 " pdb=" CA LEU 2 302 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1431 0.043 - 0.085: 381 0.085 - 0.127: 102 0.127 - 0.170: 10 0.170 - 0.212: 4 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CCV LMN C 901 " pdb=" CCR LMN C 901 " pdb=" CCT LMN C 901 " pdb=" OAU LMN C 901 " both_signs ideal model delta sigma weight residual False 2.28 2.47 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1925 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 332 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO T 333 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO T 333 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO T 333 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 530 " 0.013 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE C 530 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 530 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 530 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 530 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 530 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 530 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 2 228 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO 2 229 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO 2 229 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 229 " -0.025 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 215 2.68 - 3.24: 12086 3.24 - 3.79: 19755 3.79 - 4.35: 26475 4.35 - 4.90: 43713 Nonbonded interactions: 102244 Sorted by model distance: nonbonded pdb=" OH TYR C 782 " pdb=" OD1 ASP C 839 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR 2 67 " pdb=" OG1 THR 2 314 " model vdw 2.148 3.040 nonbonded pdb=" OD2 ASP 2 39 " pdb=" OH TYR 2 73 " model vdw 2.221 3.040 nonbonded pdb=" O ILE 2 224 " pdb=" OG1 THR 2 228 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP C 573 " pdb=" NH1 ARG C 606 " model vdw 2.261 3.120 ... (remaining 102239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 12638 Z= 0.261 Angle : 0.646 9.904 17122 Z= 0.343 Chirality : 0.042 0.212 1928 Planarity : 0.004 0.103 2118 Dihedral : 14.460 136.352 4658 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 0.23 % Allowed : 0.30 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.22), residues: 1481 helix: 1.89 (0.18), residues: 844 sheet: -0.56 (0.52), residues: 91 loop : -0.53 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 44 TYR 0.014 0.001 TYR A 194 PHE 0.032 0.001 PHE C 530 TRP 0.022 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.26 (12638) covalent geometry : angle 0.64585 / 0.34 (17122) hydrogen bonds : bond 0.14147 / 9.38 ( 707) hydrogen bonds : angle 5.59514 / 4.03 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 206 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7231 (tpt) cc_final: 0.6906 (tpt) REVERT: 2 395 TYR cc_start: 0.8272 (m-10) cc_final: 0.7956 (m-10) REVERT: C 793 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7418 (tt0) REVERT: C 798 LYS cc_start: 0.7700 (tttm) cc_final: 0.7492 (mptt) REVERT: C 805 LEU cc_start: 0.8222 (tt) cc_final: 0.7801 (mp) REVERT: C 811 ASP cc_start: 0.7662 (m-30) cc_final: 0.7315 (t0) outliers start: 3 outliers final: 2 residues processed: 207 average time/residue: 0.1054 time to fit residues: 31.8285 Evaluate side-chains 143 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 392 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.199395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145594 restraints weight = 12070.029| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.33 r_work: 0.3394 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12638 Z= 0.133 Angle : 0.536 7.218 17122 Z= 0.277 Chirality : 0.040 0.145 1928 Planarity : 0.004 0.063 2118 Dihedral : 9.681 108.177 1772 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 0.90 % Allowed : 5.20 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1481 helix: 2.18 (0.18), residues: 841 sheet: -0.37 (0.54), residues: 89 loop : -0.51 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 135 TYR 0.018 0.001 TYR 2 412 PHE 0.026 0.001 PHE C 530 TRP 0.019 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12638) covalent geometry : angle 0.53578 / 0.28 (17122) hydrogen bonds : bond 0.04217 / 2.76 ( 707) hydrogen bonds : angle 4.40013 / 3.09 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.6473 (tpt) cc_final: 0.6183 (tpt) REVERT: 2 222 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5728 (mp) REVERT: 2 395 TYR cc_start: 0.8165 (m-10) cc_final: 0.7829 (m-10) REVERT: A 66 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7371 (mt) REVERT: A 74 MET cc_start: 0.6503 (mmp) cc_final: 0.5680 (ttp) REVERT: A 82 MET cc_start: 0.7918 (ppp) cc_final: 0.7465 (ptp) REVERT: A 114 ARG cc_start: 0.7795 (mpt-90) cc_final: 0.7371 (mmm160) REVERT: C 798 LYS cc_start: 0.7397 (tttm) cc_final: 0.6856 (mptt) REVERT: C 805 LEU cc_start: 0.7478 (tt) cc_final: 0.7041 (mp) REVERT: C 811 ASP cc_start: 0.8284 (m-30) cc_final: 0.7639 (t0) REVERT: T 159 LYS cc_start: 0.7450 (ttpp) cc_final: 0.7104 (ttmm) REVERT: T 315 LYS cc_start: 0.7111 (ttpt) cc_final: 0.6803 (ttpt) outliers start: 12 outliers final: 6 residues processed: 163 average time/residue: 0.1049 time to fit residues: 24.8653 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain T residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 82 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 392 ASN 2 393 ASN b 22 ASN A 165 GLN C 607 GLN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.188216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135503 restraints weight = 12366.759| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.13 r_work: 0.3278 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12638 Z= 0.214 Angle : 0.593 8.899 17122 Z= 0.304 Chirality : 0.042 0.156 1928 Planarity : 0.004 0.053 2118 Dihedral : 9.388 95.302 1768 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 7.23 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1481 helix: 1.87 (0.18), residues: 850 sheet: -0.34 (0.50), residues: 97 loop : -0.65 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.021 0.002 TYR 2 67 PHE 0.022 0.002 PHE C 530 TRP 0.014 0.002 TRP T 30 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.21 (12638) covalent geometry : angle 0.59330 / 0.30 (17122) hydrogen bonds : bond 0.04477 / 2.91 ( 707) hydrogen bonds : angle 4.38250 / 3.08 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7326 (tp) REVERT: 2 155 MET cc_start: 0.6486 (tpt) cc_final: 0.6187 (tpt) REVERT: 2 222 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.6008 (mp) REVERT: 2 395 TYR cc_start: 0.8250 (m-10) cc_final: 0.7880 (m-10) REVERT: A 66 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 82 MET cc_start: 0.8013 (ppp) cc_final: 0.7603 (ptp) REVERT: C 682 ASP cc_start: 0.8241 (t0) cc_final: 0.7519 (t70) REVERT: C 794 GLN cc_start: 0.6556 (mt0) cc_final: 0.6319 (mt0) REVERT: C 798 LYS cc_start: 0.7457 (tttm) cc_final: 0.6852 (mptt) REVERT: C 805 LEU cc_start: 0.7527 (tt) cc_final: 0.7128 (mp) REVERT: C 811 ASP cc_start: 0.8377 (m-30) cc_final: 0.7785 (t0) REVERT: C 842 MET cc_start: 0.6511 (mtp) cc_final: 0.6003 (mtp) REVERT: T 357 ARG cc_start: 0.7191 (mtp85) cc_final: 0.6847 (mmp80) outliers start: 24 outliers final: 13 residues processed: 162 average time/residue: 0.0894 time to fit residues: 22.3111 Evaluate side-chains 156 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 74 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 392 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.195673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142068 restraints weight = 12217.003| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.32 r_work: 0.3379 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12638 Z= 0.116 Angle : 0.499 12.074 17122 Z= 0.256 Chirality : 0.039 0.138 1928 Planarity : 0.004 0.063 2118 Dihedral : 9.016 90.693 1768 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.64 % Rotamer: Outliers : 1.51 % Allowed : 8.82 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1481 helix: 2.17 (0.18), residues: 847 sheet: -0.51 (0.49), residues: 105 loop : -0.46 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 135 TYR 0.016 0.001 TYR 2 412 PHE 0.022 0.001 PHE C 599 TRP 0.011 0.001 TRP T 30 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12638) covalent geometry : angle 0.49891 / 0.26 (17122) hydrogen bonds : bond 0.03637 / 2.37 ( 707) hydrogen bonds : angle 4.10244 / 2.86 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6219 (t80) REVERT: 2 155 MET cc_start: 0.6451 (tpt) cc_final: 0.6146 (tpt) REVERT: 2 222 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6034 (mp) REVERT: 2 395 TYR cc_start: 0.8176 (m-10) cc_final: 0.7886 (m-10) REVERT: A 66 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7464 (mt) REVERT: A 82 MET cc_start: 0.8043 (ppp) cc_final: 0.7629 (ptp) REVERT: C 438 MET cc_start: 0.3279 (ttp) cc_final: 0.3018 (mtp) REVERT: C 682 ASP cc_start: 0.8217 (t0) cc_final: 0.7457 (t70) REVERT: C 695 GLN cc_start: 0.7623 (mt0) cc_final: 0.7329 (mt0) REVERT: C 794 GLN cc_start: 0.6488 (mt0) cc_final: 0.6173 (mt0) REVERT: C 798 LYS cc_start: 0.7351 (tttm) cc_final: 0.6788 (mptt) REVERT: C 805 LEU cc_start: 0.7514 (tt) cc_final: 0.7146 (mp) REVERT: C 811 ASP cc_start: 0.8339 (m-30) cc_final: 0.7834 (t0) REVERT: C 842 MET cc_start: 0.6475 (mtp) cc_final: 0.5906 (mtp) REVERT: T 354 ARG cc_start: 0.6956 (mtm110) cc_final: 0.6746 (mtm110) REVERT: T 356 LEU cc_start: 0.7596 (mt) cc_final: 0.7370 (mt) outliers start: 20 outliers final: 12 residues processed: 155 average time/residue: 0.1056 time to fit residues: 24.3244 Evaluate side-chains 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 50.0000 chunk 119 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.194677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140241 restraints weight = 12273.634| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.38 r_work: 0.3372 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12638 Z= 0.119 Angle : 0.501 12.144 17122 Z= 0.255 Chirality : 0.039 0.137 1928 Planarity : 0.004 0.057 2118 Dihedral : 8.677 83.703 1768 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 9.50 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.22), residues: 1481 helix: 2.24 (0.18), residues: 854 sheet: -0.51 (0.49), residues: 105 loop : -0.40 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 50 TYR 0.017 0.001 TYR 2 412 PHE 0.022 0.001 PHE C 599 TRP 0.012 0.001 TRP T 30 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12638) covalent geometry : angle 0.50060 / 0.26 (17122) hydrogen bonds : bond 0.03552 / 2.31 ( 707) hydrogen bonds : angle 4.03474 / 2.82 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6473 (t80) REVERT: 2 155 MET cc_start: 0.6365 (tpt) cc_final: 0.6127 (tpt) REVERT: 2 222 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.5880 (mp) REVERT: 2 395 TYR cc_start: 0.8066 (m-10) cc_final: 0.7789 (m-10) REVERT: A 66 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7391 (mt) REVERT: A 82 MET cc_start: 0.7922 (ppp) cc_final: 0.7600 (ptp) REVERT: C 438 MET cc_start: 0.3230 (ttp) cc_final: 0.2961 (mtp) REVERT: C 682 ASP cc_start: 0.8224 (t0) cc_final: 0.7423 (t70) REVERT: C 695 GLN cc_start: 0.7567 (mt0) cc_final: 0.7281 (mt0) REVERT: C 797 GLU cc_start: 0.6321 (mt-10) cc_final: 0.6031 (mt-10) REVERT: C 805 LEU cc_start: 0.7458 (tt) cc_final: 0.7104 (mp) REVERT: C 811 ASP cc_start: 0.8362 (m-30) cc_final: 0.7855 (t0) REVERT: C 842 MET cc_start: 0.6491 (mtp) cc_final: 0.5949 (mtp) outliers start: 27 outliers final: 16 residues processed: 158 average time/residue: 0.0965 time to fit residues: 23.2740 Evaluate side-chains 157 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 GLN T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.194120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140155 restraints weight = 12245.174| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.30 r_work: 0.3346 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12638 Z= 0.120 Angle : 0.503 13.873 17122 Z= 0.254 Chirality : 0.039 0.136 1928 Planarity : 0.004 0.056 2118 Dihedral : 8.444 80.639 1768 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 10.70 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.22), residues: 1481 helix: 2.28 (0.17), residues: 854 sheet: -0.76 (0.48), residues: 113 loop : -0.32 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.016 0.001 TYR 2 412 PHE 0.018 0.001 PHE C 599 TRP 0.012 0.001 TRP T 30 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12638) covalent geometry : angle 0.50306 / 0.25 (17122) hydrogen bonds : bond 0.03502 / 2.27 ( 707) hydrogen bonds : angle 3.99505 / 2.79 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6524 (t80) REVERT: 2 155 MET cc_start: 0.6413 (tpt) cc_final: 0.6189 (tpt) REVERT: 2 222 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6037 (mp) REVERT: A 50 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7368 (ttm110) REVERT: A 82 MET cc_start: 0.7957 (ppp) cc_final: 0.7610 (ptp) REVERT: C 438 MET cc_start: 0.3199 (ttp) cc_final: 0.2744 (ttp) REVERT: C 682 ASP cc_start: 0.8283 (t0) cc_final: 0.7513 (t70) REVERT: C 695 GLN cc_start: 0.7642 (mt0) cc_final: 0.7373 (mt0) REVERT: C 797 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6124 (mt-10) REVERT: C 805 LEU cc_start: 0.7498 (tt) cc_final: 0.7142 (mp) REVERT: C 811 ASP cc_start: 0.8384 (m-30) cc_final: 0.7895 (t0) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.1013 time to fit residues: 24.3521 Evaluate side-chains 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 664 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 283 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 227 ASN T 151 ASN T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.187070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132093 restraints weight = 12387.847| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.44 r_work: 0.3242 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12638 Z= 0.282 Angle : 0.667 16.263 17122 Z= 0.337 Chirality : 0.045 0.163 1928 Planarity : 0.004 0.044 2118 Dihedral : 8.940 77.906 1768 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 1.81 % Allowed : 11.76 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.22), residues: 1481 helix: 1.73 (0.17), residues: 851 sheet: -0.82 (0.50), residues: 98 loop : -0.64 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.023 0.002 TYR 2 67 PHE 0.021 0.002 PHE 2 74 TRP 0.019 0.002 TRP T 102 HIS 0.007 0.002 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.28 (12638) covalent geometry : angle 0.66652 / 0.34 (17122) hydrogen bonds : bond 0.04699 / 3.03 ( 707) hydrogen bonds : angle 4.37574 / 3.06 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 47 LEU cc_start: 0.7500 (mp) cc_final: 0.7130 (mt) REVERT: 2 73 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6263 (t80) REVERT: 2 107 PHE cc_start: 0.6546 (m-80) cc_final: 0.6289 (m-80) REVERT: 2 155 MET cc_start: 0.6544 (tpt) cc_final: 0.6302 (tpt) REVERT: 2 160 MET cc_start: 0.6832 (mmt) cc_final: 0.6567 (mmp) REVERT: 2 222 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6243 (mp) REVERT: 2 395 TYR cc_start: 0.8185 (m-10) cc_final: 0.7898 (m-10) REVERT: A 82 MET cc_start: 0.8069 (ppp) cc_final: 0.7715 (ptp) REVERT: C 438 MET cc_start: 0.3228 (ttp) cc_final: 0.2788 (ttp) REVERT: C 682 ASP cc_start: 0.8503 (t0) cc_final: 0.8086 (t0) REVERT: C 695 GLN cc_start: 0.7728 (mt0) cc_final: 0.7324 (mt0) REVERT: C 798 LYS cc_start: 0.7422 (tttm) cc_final: 0.6822 (mptt) REVERT: C 805 LEU cc_start: 0.7576 (tt) cc_final: 0.7232 (mp) REVERT: C 811 ASP cc_start: 0.8526 (m-30) cc_final: 0.7829 (t0) REVERT: C 842 MET cc_start: 0.6558 (mtp) cc_final: 0.6005 (mtp) outliers start: 24 outliers final: 15 residues processed: 160 average time/residue: 0.0958 time to fit residues: 22.9327 Evaluate side-chains 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain T residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 0.0770 chunk 95 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 54 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.193503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139575 restraints weight = 12160.865| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.09 r_work: 0.3380 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12638 Z= 0.115 Angle : 0.515 13.639 17122 Z= 0.263 Chirality : 0.039 0.135 1928 Planarity : 0.004 0.062 2118 Dihedral : 8.498 76.431 1768 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.58 % Allowed : 11.76 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1481 helix: 2.16 (0.17), residues: 848 sheet: -0.85 (0.48), residues: 109 loop : -0.43 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.019 0.001 TYR 2 412 PHE 0.026 0.001 PHE C 599 TRP 0.013 0.001 TRP T 102 HIS 0.005 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12638) covalent geometry : angle 0.51520 / 0.26 (17122) hydrogen bonds : bond 0.03536 / 2.30 ( 707) hydrogen bonds : angle 4.06958 / 2.83 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6582 (t80) REVERT: 2 155 MET cc_start: 0.6492 (tpt) cc_final: 0.6243 (tpt) REVERT: 2 160 MET cc_start: 0.6773 (mmt) cc_final: 0.6569 (mmp) REVERT: 2 222 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5979 (mp) REVERT: 2 395 TYR cc_start: 0.8127 (m-10) cc_final: 0.7874 (m-10) REVERT: A 50 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7323 (ttm110) REVERT: A 82 MET cc_start: 0.8021 (ppp) cc_final: 0.7616 (ptp) REVERT: A 183 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7596 (ttp-170) REVERT: C 438 MET cc_start: 0.3231 (ttp) cc_final: 0.2768 (ttp) REVERT: C 682 ASP cc_start: 0.8456 (t0) cc_final: 0.7896 (t0) REVERT: C 695 GLN cc_start: 0.7642 (mt0) cc_final: 0.7365 (mt0) REVERT: C 798 LYS cc_start: 0.7249 (tttm) cc_final: 0.6543 (mptt) REVERT: C 805 LEU cc_start: 0.7586 (tt) cc_final: 0.7255 (mp) REVERT: C 811 ASP cc_start: 0.8483 (m-30) cc_final: 0.7786 (t0) REVERT: C 842 MET cc_start: 0.6638 (mtp) cc_final: 0.5976 (mtp) REVERT: T 9 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7301 (ttp-110) REVERT: T 47 LYS cc_start: 0.6524 (tttm) cc_final: 0.6242 (tttp) REVERT: T 194 GLU cc_start: 0.7092 (pt0) cc_final: 0.6874 (pt0) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.1004 time to fit residues: 23.6556 Evaluate side-chains 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 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 = 0.4153 r_free = 0.4153 target = 0.194500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140077 restraints weight = 12142.993| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.29 r_work: 0.3367 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12638 Z= 0.110 Angle : 0.505 13.982 17122 Z= 0.256 Chirality : 0.039 0.138 1928 Planarity : 0.004 0.059 2118 Dihedral : 8.134 72.875 1768 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 12.43 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1481 helix: 2.40 (0.18), residues: 848 sheet: -0.94 (0.47), residues: 113 loop : -0.27 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.019 0.001 TYR 2 412 PHE 0.024 0.001 PHE C 599 TRP 0.013 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12638) covalent geometry : angle 0.50505 / 0.26 (17122) hydrogen bonds : bond 0.03372 / 2.19 ( 707) hydrogen bonds : angle 3.97193 / 2.77 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6894 (t80) REVERT: 2 155 MET cc_start: 0.6641 (tpt) cc_final: 0.6358 (tpt) REVERT: 2 160 MET cc_start: 0.6677 (mmt) cc_final: 0.6420 (mmp) REVERT: 2 222 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6097 (mp) REVERT: A 50 ARG cc_start: 0.7620 (ttm110) cc_final: 0.7044 (mtt90) REVERT: A 82 MET cc_start: 0.8001 (ppp) cc_final: 0.7613 (ptp) REVERT: C 438 MET cc_start: 0.3236 (ttp) cc_final: 0.2794 (ttp) REVERT: C 682 ASP cc_start: 0.8460 (t0) cc_final: 0.7930 (t0) REVERT: C 695 GLN cc_start: 0.7602 (mt0) cc_final: 0.7361 (mt0) REVERT: C 798 LYS cc_start: 0.7341 (tttm) cc_final: 0.6715 (mptt) REVERT: C 805 LEU cc_start: 0.7598 (tt) cc_final: 0.7289 (mp) REVERT: C 811 ASP cc_start: 0.8523 (m-30) cc_final: 0.7957 (t0) REVERT: T 47 LYS cc_start: 0.6576 (tttm) cc_final: 0.6315 (tttp) REVERT: T 194 GLU cc_start: 0.7085 (pt0) cc_final: 0.6866 (pt0) outliers start: 17 outliers final: 11 residues processed: 154 average time/residue: 0.0984 time to fit residues: 23.0273 Evaluate side-chains 145 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 227 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.193890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139140 restraints weight = 12196.373| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.32 r_work: 0.3357 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12638 Z= 0.121 Angle : 0.524 14.239 17122 Z= 0.263 Chirality : 0.039 0.144 1928 Planarity : 0.003 0.046 2118 Dihedral : 8.009 71.892 1768 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 1.58 % Allowed : 12.13 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.22), residues: 1481 helix: 2.41 (0.17), residues: 848 sheet: -0.93 (0.47), residues: 113 loop : -0.30 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.018 0.001 TYR 2 312 PHE 0.024 0.001 PHE C 599 TRP 0.015 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (12638) covalent geometry : angle 0.52404 / 0.26 (17122) hydrogen bonds : bond 0.03453 / 2.23 ( 707) hydrogen bonds : angle 3.96765 / 2.77 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6536 (t80) REVERT: 2 155 MET cc_start: 0.6472 (tpt) cc_final: 0.6170 (tpt) REVERT: 2 160 MET cc_start: 0.6668 (mmt) cc_final: 0.6448 (mmp) REVERT: 2 222 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6142 (mp) REVERT: A 82 MET cc_start: 0.8002 (ppp) cc_final: 0.7612 (ptp) REVERT: C 438 MET cc_start: 0.3228 (ttp) cc_final: 0.2786 (ttp) REVERT: C 682 ASP cc_start: 0.8453 (t0) cc_final: 0.7922 (t0) REVERT: C 695 GLN cc_start: 0.7608 (mt0) cc_final: 0.7362 (mt0) REVERT: C 798 LYS cc_start: 0.7325 (tttm) cc_final: 0.6714 (mptt) REVERT: C 805 LEU cc_start: 0.7593 (tt) cc_final: 0.7287 (mp) REVERT: C 811 ASP cc_start: 0.8522 (m-30) cc_final: 0.7970 (t0) REVERT: T 47 LYS cc_start: 0.6569 (tttm) cc_final: 0.6308 (tttp) REVERT: T 194 GLU cc_start: 0.7095 (pt0) cc_final: 0.6868 (pt0) outliers start: 21 outliers final: 13 residues processed: 154 average time/residue: 0.1015 time to fit residues: 23.5852 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.194598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140183 restraints weight = 12094.694| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.33 r_work: 0.3371 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12638 Z= 0.111 Angle : 0.519 15.245 17122 Z= 0.260 Chirality : 0.039 0.163 1928 Planarity : 0.004 0.061 2118 Dihedral : 7.833 73.716 1768 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 12.74 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1481 helix: 2.40 (0.17), residues: 862 sheet: -0.90 (0.47), residues: 113 loop : -0.29 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 50 TYR 0.018 0.001 TYR 2 412 PHE 0.023 0.001 PHE C 599 TRP 0.015 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12638) covalent geometry : angle 0.51898 / 0.26 (17122) hydrogen bonds : bond 0.03362 / 2.17 ( 707) hydrogen bonds : angle 3.94500 / 2.75 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3530.89 seconds wall clock time: 61 minutes 2.97 seconds (3662.97 seconds total)