Starting phenix.real_space_refine on Wed Mar 4 11:32:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zkq_14765/03_2026/7zkq_14765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zkq_14765/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zkq_14765/03_2026/7zkq_14765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zkq_14765/03_2026/7zkq_14765.map" model { file = "/net/cci-nas-00/data/ceres_data/7zkq_14765/03_2026/7zkq_14765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zkq_14765/03_2026/7zkq_14765.cif" } 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-5986/lib/python3.9/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: 19 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: 43 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.44, per 1000 atoms: 0.20 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: 0.97 Conformation dependent library (CDL) restraints added in 457.2 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: 0.25 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: 2.08 Time building geometry restraints manager: 1.20 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 - 34.11: 7383 34.11 - 68.22: 207 68.22 - 102.34: 38 102.34 - 136.45: 18 136.45 - 170.56: 2 Dihedral angle restraints: 7648 sinusoidal: 3238 harmonic: 4410 Sorted by residual: dihedral pdb=" C3 PLC T 401 " pdb=" C1 PLC T 401 " pdb=" C2 PLC T 401 " pdb=" O3P PLC T 401 " ideal model delta sinusoidal sigma weight residual 67.16 -122.28 -170.56 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC T 401 " pdb=" C1 PLC T 401 " pdb=" C2 PLC T 401 " pdb=" O3P PLC T 401 " ideal model delta sinusoidal sigma weight residual -55.71 112.91 -168.62 1 3.00e+01 1.11e-03 2.11e+01 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 ... (remaining 7645 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: 0.750 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 17.818 170.559 4814 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 covalent geometry : bond 0.00520 (12638) covalent geometry : angle 0.64585 (17122) hydrogen bonds : bond 0.14147 ( 707) hydrogen bonds : angle 5.59514 ( 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 : 0.409 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: 0.1090 time to fit residues: 32.4799 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 : 0.419 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4155 r_free = 0.4155 target = 0.195535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143869 restraints weight = 12034.573| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.07 r_work: 0.3426 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12638 Z= 0.135 Angle : 0.575 8.972 17122 Z= 0.286 Chirality : 0.041 0.181 1928 Planarity : 0.004 0.063 2118 Dihedral : 14.372 166.705 1928 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 0.98 % Allowed : 5.20 % Favored : 93.82 % 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: 1.54 (0.22), residues: 1481 helix: 2.17 (0.18), residues: 843 sheet: -0.40 (0.53), residues: 89 loop : -0.54 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 135 TYR 0.018 0.001 TYR 2 412 PHE 0.028 0.001 PHE C 530 TRP 0.021 0.001 TRP T 102 HIS 0.005 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00307 (12638) covalent geometry : angle 0.57469 (17122) hydrogen bonds : bond 0.04009 ( 707) hydrogen bonds : angle 4.34778 ( 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 171 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.6498 (tpt) cc_final: 0.6203 (tpt) REVERT: 2 222 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5675 (mp) REVERT: 2 395 TYR cc_start: 0.8176 (m-10) cc_final: 0.7850 (m-10) REVERT: A 66 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7407 (mt) REVERT: A 74 MET cc_start: 0.6535 (mmp) cc_final: 0.5687 (ttp) REVERT: A 82 MET cc_start: 0.7924 (ppp) cc_final: 0.7461 (ptp) REVERT: A 114 ARG cc_start: 0.7748 (mpt-90) cc_final: 0.7325 (mmm160) REVERT: C 798 LYS cc_start: 0.7385 (tttm) cc_final: 0.6840 (mptt) REVERT: C 805 LEU cc_start: 0.7496 (tt) cc_final: 0.7066 (mp) REVERT: C 811 ASP cc_start: 0.8274 (m-30) cc_final: 0.7634 (t0) REVERT: T 159 LYS cc_start: 0.7457 (ttpp) cc_final: 0.7116 (ttmm) REVERT: T 315 LYS cc_start: 0.7142 (ttpt) cc_final: 0.6829 (ttpt) REVERT: T 357 ARG cc_start: 0.7190 (mtp85) cc_final: 0.6930 (mtp85) outliers start: 13 outliers final: 7 residues processed: 166 average time/residue: 0.1057 time to fit residues: 25.5659 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain T residue 283 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: 0.0050 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: 8.9990 chunk 134 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 392 ASN b 22 ASN C 607 GLN ** 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 = 0.4131 r_free = 0.4131 target = 0.192175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139738 restraints weight = 12257.021| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.98 r_work: 0.3367 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12638 Z= 0.164 Angle : 0.557 8.629 17122 Z= 0.283 Chirality : 0.040 0.148 1928 Planarity : 0.004 0.050 2118 Dihedral : 12.369 167.377 1924 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 1.58 % Allowed : 7.16 % Favored : 91.26 % 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: 1.48 (0.22), residues: 1481 helix: 2.10 (0.18), residues: 844 sheet: -0.30 (0.50), residues: 97 loop : -0.56 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.018 0.001 TYR 2 67 PHE 0.023 0.002 PHE C 530 TRP 0.013 0.001 TRP T 30 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd covalent geometry : bond 0.00395 (12638) covalent geometry : angle 0.55719 (17122) hydrogen bonds : bond 0.04114 ( 707) hydrogen bonds : angle 4.23369 ( 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 163 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7295 (tp) REVERT: 2 155 MET cc_start: 0.6524 (tpt) cc_final: 0.6214 (tpt) REVERT: 2 222 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6007 (mp) REVERT: 2 395 TYR cc_start: 0.8216 (m-10) cc_final: 0.7894 (m-10) REVERT: A 66 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7507 (mt) REVERT: A 82 MET cc_start: 0.8037 (ppp) cc_final: 0.7614 (ptp) REVERT: C 682 ASP cc_start: 0.8212 (t0) cc_final: 0.7485 (t70) REVERT: C 794 GLN cc_start: 0.6530 (mt0) cc_final: 0.6326 (mt0) REVERT: C 798 LYS cc_start: 0.7423 (tttm) cc_final: 0.6855 (mptt) REVERT: C 805 LEU cc_start: 0.7577 (tt) cc_final: 0.7181 (mp) REVERT: C 811 ASP cc_start: 0.8324 (m-30) cc_final: 0.7706 (t0) REVERT: C 821 ASN cc_start: 0.6403 (p0) cc_final: 0.6128 (p0) REVERT: C 842 MET cc_start: 0.6513 (mtp) cc_final: 0.6061 (mtp) outliers start: 21 outliers final: 11 residues processed: 153 average time/residue: 0.0936 time to fit residues: 21.3821 Evaluate side-chains 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 303 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 45 CYS Chi-restraints excluded: chain T residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 392 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 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 = 0.4165 r_free = 0.4165 target = 0.195696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142019 restraints weight = 12192.749| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.31 r_work: 0.3379 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12638 Z= 0.122 Angle : 0.505 12.959 17122 Z= 0.257 Chirality : 0.038 0.136 1928 Planarity : 0.003 0.048 2118 Dihedral : 11.894 168.183 1924 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.58 % Allowed : 8.67 % Favored : 89.75 % 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: 1.61 (0.22), residues: 1481 helix: 2.20 (0.18), residues: 853 sheet: -0.51 (0.49), residues: 105 loop : -0.50 (0.28), residues: 523 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 0.019 0.001 PHE C 530 TRP 0.011 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00284 (12638) covalent geometry : angle 0.50532 (17122) hydrogen bonds : bond 0.03622 ( 707) hydrogen bonds : angle 4.06231 ( 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 166 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.6426 (tpt) cc_final: 0.6174 (tpt) REVERT: 2 222 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6019 (mp) REVERT: 2 395 TYR cc_start: 0.8180 (m-10) cc_final: 0.7882 (m-10) REVERT: A 66 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7478 (mt) REVERT: A 82 MET cc_start: 0.7965 (ppp) cc_final: 0.7604 (ptp) REVERT: A 183 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7318 (ttp-170) REVERT: C 438 MET cc_start: 0.3264 (ttp) cc_final: 0.2986 (mtp) REVERT: C 682 ASP cc_start: 0.8193 (t0) cc_final: 0.7426 (t70) REVERT: C 695 GLN cc_start: 0.7612 (mt0) cc_final: 0.7318 (mt0) REVERT: C 805 LEU cc_start: 0.7531 (tt) cc_final: 0.7163 (mp) REVERT: C 811 ASP cc_start: 0.8328 (m-30) cc_final: 0.7839 (t0) REVERT: C 842 MET cc_start: 0.6577 (mtp) cc_final: 0.6088 (mtp) REVERT: T 357 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6759 (mtp85) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 0.0972 time to fit residues: 22.9243 Evaluate side-chains 150 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 25 optimal weight: 0.0050 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 72 optimal weight: 50.0000 chunk 119 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 794 GLN ** 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 = 0.4173 r_free = 0.4173 target = 0.196756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143053 restraints weight = 12252.143| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.34 r_work: 0.3392 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12638 Z= 0.107 Angle : 0.490 12.818 17122 Z= 0.249 Chirality : 0.038 0.132 1928 Planarity : 0.003 0.046 2118 Dihedral : 11.602 169.029 1924 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 1.73 % Allowed : 10.10 % Favored : 88.17 % 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: 1.76 (0.22), residues: 1481 helix: 2.34 (0.18), residues: 853 sheet: -0.81 (0.48), residues: 113 loop : -0.35 (0.29), residues: 515 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 0.017 0.001 PHE C 530 TRP 0.011 0.001 TRP T 30 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00240 (12638) covalent geometry : angle 0.49046 (17122) hydrogen bonds : bond 0.03404 ( 707) hydrogen bonds : angle 3.97235 ( 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 164 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6532 (t80) REVERT: 2 155 MET cc_start: 0.6400 (tpt) cc_final: 0.6182 (tpt) REVERT: 2 222 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6005 (mp) REVERT: A 50 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7381 (ttm110) REVERT: A 82 MET cc_start: 0.7971 (ppp) cc_final: 0.7625 (ptp) REVERT: A 183 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7360 (ttp-170) REVERT: C 438 MET cc_start: 0.3209 (ttp) cc_final: 0.2740 (ttp) REVERT: C 682 ASP cc_start: 0.8185 (t0) cc_final: 0.7427 (t70) REVERT: C 695 GLN cc_start: 0.7581 (mt0) cc_final: 0.7337 (mt0) REVERT: C 805 LEU cc_start: 0.7501 (tt) cc_final: 0.7142 (mp) REVERT: C 811 ASP cc_start: 0.8368 (m-30) cc_final: 0.7874 (t0) REVERT: T 357 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6845 (mtp85) outliers start: 23 outliers final: 16 residues processed: 154 average time/residue: 0.0892 time to fit residues: 21.0342 Evaluate side-chains 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 303 ASN Chi-restraints excluded: chain 2 residue 428 LEU 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 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 Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.0670 chunk 113 optimal weight: 1.9990 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: 0.2980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.196649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143028 restraints weight = 12216.899| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.34 r_work: 0.3375 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12638 Z= 0.105 Angle : 0.486 13.580 17122 Z= 0.245 Chirality : 0.038 0.132 1928 Planarity : 0.003 0.067 2118 Dihedral : 11.411 168.778 1924 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 10.93 % Favored : 87.42 % 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: 1.81 (0.22), residues: 1481 helix: 2.38 (0.17), residues: 857 sheet: -0.83 (0.47), residues: 113 loop : -0.35 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.017 0.001 TYR 2 412 PHE 0.024 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 covalent geometry : bond 0.00235 (12638) covalent geometry : angle 0.48648 (17122) hydrogen bonds : bond 0.03344 ( 707) hydrogen bonds : angle 3.92565 ( 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 156 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6831 (t80) REVERT: 2 155 MET cc_start: 0.6348 (tpt) cc_final: 0.6131 (tpt) REVERT: 2 222 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6093 (mp) REVERT: 2 391 LEU cc_start: 0.7871 (mt) cc_final: 0.7611 (mt) REVERT: A 82 MET cc_start: 0.7968 (ppp) cc_final: 0.7625 (ptp) REVERT: A 183 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.7408 (ttp-170) REVERT: C 438 MET cc_start: 0.3226 (ttp) cc_final: 0.2776 (ttp) REVERT: C 682 ASP cc_start: 0.8232 (t0) cc_final: 0.7459 (t70) REVERT: C 695 GLN cc_start: 0.7541 (mt0) cc_final: 0.7303 (mt0) REVERT: C 805 LEU cc_start: 0.7514 (tt) cc_final: 0.7181 (mp) REVERT: C 811 ASP cc_start: 0.8375 (m-30) cc_final: 0.7865 (t0) REVERT: T 357 ARG cc_start: 0.7137 (mtp85) cc_final: 0.6820 (mtp85) outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.0931 time to fit residues: 20.7804 Evaluate side-chains 150 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 58 LEU 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 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 Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 0.0980 chunk 90 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** 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 = 0.193943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.140171 restraints weight = 12197.838| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.10 r_work: 0.3366 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2302 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= 0.132 Angle : 0.512 14.546 17122 Z= 0.257 Chirality : 0.039 0.138 1928 Planarity : 0.004 0.061 2118 Dihedral : 11.311 167.054 1924 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 1.81 % Allowed : 11.08 % Favored : 87.11 % 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: 2.31 (0.18), residues: 858 sheet: -0.90 (0.47), residues: 115 loop : -0.36 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.015 0.001 TYR C 646 PHE 0.024 0.001 PHE C 599 TRP 0.013 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd covalent geometry : bond 0.00314 (12638) covalent geometry : angle 0.51218 (17122) hydrogen bonds : bond 0.03548 ( 707) hydrogen bonds : angle 3.97470 ( 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 169 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6880 (t80) REVERT: 2 155 MET cc_start: 0.6444 (tpt) cc_final: 0.6215 (tpt) REVERT: 2 222 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.5966 (mp) REVERT: A 50 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7112 (mtt90) REVERT: A 82 MET cc_start: 0.7981 (ppp) cc_final: 0.7627 (ptp) REVERT: C 438 MET cc_start: 0.3215 (ttp) cc_final: 0.2774 (ttp) REVERT: C 682 ASP cc_start: 0.8320 (t0) cc_final: 0.7567 (t70) REVERT: C 695 GLN cc_start: 0.7602 (mt0) cc_final: 0.7342 (mt0) REVERT: C 805 LEU cc_start: 0.7555 (tt) cc_final: 0.7224 (mp) REVERT: C 811 ASP cc_start: 0.8390 (m-30) cc_final: 0.7884 (t0) REVERT: T 357 ARG cc_start: 0.7246 (mtp85) cc_final: 0.6903 (mtp85) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 0.0863 time to fit residues: 20.9190 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 0.0050 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139820 restraints weight = 12133.440| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.37 r_work: 0.3366 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2407 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= 0.128 Angle : 0.515 13.720 17122 Z= 0.261 Chirality : 0.039 0.144 1928 Planarity : 0.003 0.043 2118 Dihedral : 11.223 166.859 1924 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 1.73 % Allowed : 11.76 % Favored : 86.51 % 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: 2.32 (0.17), residues: 858 sheet: -0.99 (0.47), residues: 115 loop : -0.35 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.016 0.001 TYR 2 157 PHE 0.025 0.001 PHE C 599 TRP 0.014 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 Details of bonding type rmsd covalent geometry : bond 0.00300 (12638) covalent geometry : angle 0.51542 (17122) hydrogen bonds : bond 0.03492 ( 707) hydrogen bonds : angle 3.95720 ( 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 162 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6836 (t80) REVERT: 2 155 MET cc_start: 0.6376 (tpt) cc_final: 0.6163 (tpt) REVERT: 2 222 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.5968 (mp) REVERT: 2 395 TYR cc_start: 0.8112 (m-10) cc_final: 0.7777 (m-10) REVERT: A 82 MET cc_start: 0.7926 (ppp) cc_final: 0.7603 (ptp) REVERT: C 438 MET cc_start: 0.3249 (ttp) cc_final: 0.2794 (ttp) REVERT: C 695 GLN cc_start: 0.7596 (mt0) cc_final: 0.7307 (mt0) REVERT: C 805 LEU cc_start: 0.7476 (tt) cc_final: 0.7156 (mp) REVERT: C 811 ASP cc_start: 0.8403 (m-30) cc_final: 0.7881 (t0) REVERT: T 9 ARG cc_start: 0.7384 (ttm110) cc_final: 0.7138 (ttp-110) REVERT: T 357 ARG cc_start: 0.7136 (mtp85) cc_final: 0.6803 (mtp85) outliers start: 23 outliers final: 15 residues processed: 152 average time/residue: 0.0906 time to fit residues: 20.7951 Evaluate side-chains 153 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4163 r_free = 0.4163 target = 0.195643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141524 restraints weight = 12131.335| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.37 r_work: 0.3386 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12638 Z= 0.108 Angle : 0.495 14.438 17122 Z= 0.250 Chirality : 0.038 0.140 1928 Planarity : 0.003 0.062 2118 Dihedral : 11.060 166.981 1924 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 1.36 % Allowed : 12.06 % Favored : 86.59 % 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 (0.23), residues: 1481 helix: 2.43 (0.17), residues: 862 sheet: -1.01 (0.46), residues: 115 loop : -0.30 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.017 0.001 TYR 2 412 PHE 0.022 0.001 PHE C 599 TRP 0.015 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 Details of bonding type rmsd covalent geometry : bond 0.00242 (12638) covalent geometry : angle 0.49464 (17122) hydrogen bonds : bond 0.03304 ( 707) hydrogen bonds : angle 3.89955 ( 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 154 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6828 (t80) REVERT: 2 155 MET cc_start: 0.6361 (tpt) cc_final: 0.6134 (tpt) REVERT: 2 222 ILE cc_start: 0.6434 (OUTLIER) cc_final: 0.5978 (mp) REVERT: A 82 MET cc_start: 0.7950 (ppp) cc_final: 0.7587 (ptp) REVERT: A 183 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7576 (ttp-170) REVERT: C 438 MET cc_start: 0.3235 (ttp) cc_final: 0.2799 (ttp) REVERT: C 682 ASP cc_start: 0.8406 (t0) cc_final: 0.7894 (t0) REVERT: C 695 GLN cc_start: 0.7646 (mt0) cc_final: 0.7343 (mt0) REVERT: C 805 LEU cc_start: 0.7470 (tt) cc_final: 0.7157 (mp) REVERT: C 811 ASP cc_start: 0.8445 (m-30) cc_final: 0.7846 (t0) outliers start: 18 outliers final: 14 residues processed: 148 average time/residue: 0.0859 time to fit residues: 19.7655 Evaluate side-chains 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 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: 20.0000 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.192746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138836 restraints weight = 12227.348| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.10 r_work: 0.3309 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12638 Z= 0.150 Angle : 0.541 15.176 17122 Z= 0.272 Chirality : 0.040 0.138 1928 Planarity : 0.003 0.040 2118 Dihedral : 11.126 165.175 1924 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 1.51 % Allowed : 12.43 % Favored : 86.06 % 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: 1.66 (0.22), residues: 1481 helix: 2.25 (0.17), residues: 868 sheet: -1.09 (0.46), residues: 115 loop : -0.39 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 50 TYR 0.020 0.001 TYR 2 312 PHE 0.022 0.001 PHE C 599 TRP 0.020 0.001 TRP T 102 HIS 0.005 0.001 HIS 2 320 Details of bonding type rmsd covalent geometry : bond 0.00361 (12638) covalent geometry : angle 0.54068 (17122) hydrogen bonds : bond 0.03660 ( 707) hydrogen bonds : angle 4.00214 ( 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 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6799 (t80) REVERT: 2 155 MET cc_start: 0.6506 (tpt) cc_final: 0.6201 (tpt) REVERT: 2 222 ILE cc_start: 0.6451 (OUTLIER) cc_final: 0.5992 (mp) REVERT: A 82 MET cc_start: 0.7979 (ppp) cc_final: 0.7627 (ptp) REVERT: C 438 MET cc_start: 0.3128 (ttp) cc_final: 0.2685 (ttp) REVERT: C 695 GLN cc_start: 0.7713 (mt0) cc_final: 0.7390 (mt0) REVERT: C 805 LEU cc_start: 0.7543 (tt) cc_final: 0.7224 (mp) REVERT: C 811 ASP cc_start: 0.8455 (m-30) cc_final: 0.7885 (t0) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 0.0850 time to fit residues: 19.4247 Evaluate side-chains 146 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 664 ASP Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 283 LEU Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 0.0770 chunk 96 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 227 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 GLN ** 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 = 0.4157 r_free = 0.4157 target = 0.195084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141177 restraints weight = 12096.317| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.30 r_work: 0.3378 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2584 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 : 0.510 14.380 17122 Z= 0.257 Chirality : 0.038 0.155 1928 Planarity : 0.004 0.065 2118 Dihedral : 11.025 166.016 1924 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 1.43 % Allowed : 12.28 % 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: 858 sheet: -1.08 (0.46), residues: 115 loop : -0.31 (0.29), residues: 508 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 0.017 0.001 TRP T 102 HIS 0.005 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00251 (12638) covalent geometry : angle 0.51012 (17122) hydrogen bonds : bond 0.03377 ( 707) hydrogen bonds : angle 3.92849 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.09 seconds wall clock time: 60 minutes 59.91 seconds (3659.91 seconds total)