Starting phenix.real_space_refine on Thu Jul 31 08:36:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zkq_14765/07_2025/7zkq_14765.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zkq_14765/07_2025/7zkq_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_14765/07_2025/7zkq_14765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2025/7zkq_14765.map" model { file = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2025/7zkq_14765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zkq_14765/07_2025/7zkq_14765.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.92, per 1000 atoms: 0.56 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.46 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: 4.04 Time building geometry restraints manager: 3.38 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: 0.500 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.400 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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 : 9.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (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 TRP 0.022 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.032 0.001 PHE C 530 TYR 0.014 0.001 TYR A 194 ARG 0.007 0.000 ARG T 44 Details of bonding type rmsd hydrogen bonds : bond 0.14147 ( 707) hydrogen bonds : angle 5.59514 ( 2043) covalent geometry : bond 0.00520 (12638) covalent geometry : angle 0.64585 (17122) *********************** 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 : 2.029 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: 0.2540 time to fit residues: 75.2650 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 : 1.224 ------------------------------------------------------------------------------- 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 124 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 50.0000 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.197829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140558 restraints weight = 11993.653| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.68 r_work: 0.3405 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12638 Z= 0.135 Angle : 0.571 8.959 17122 Z= 0.285 Chirality : 0.041 0.169 1928 Planarity : 0.004 0.062 2118 Dihedral : 14.576 166.838 1928 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 0.90 % Allowed : 5.12 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1481 helix: 2.19 (0.18), residues: 843 sheet: -0.39 (0.53), residues: 89 loop : -0.52 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 102 HIS 0.005 0.001 HIS C 583 PHE 0.027 0.001 PHE C 530 TYR 0.019 0.001 TYR 2 412 ARG 0.005 0.001 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 707) hydrogen bonds : angle 4.36389 ( 2043) covalent geometry : bond 0.00303 (12638) covalent geometry : angle 0.57057 (17122) *********************** 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 172 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.6359 (tpt) cc_final: 0.6072 (tpt) REVERT: 2 222 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5614 (mp) REVERT: 2 395 TYR cc_start: 0.8119 (m-10) cc_final: 0.7804 (m-10) REVERT: A 66 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7328 (mt) REVERT: A 74 MET cc_start: 0.6490 (mmp) cc_final: 0.5678 (ttp) REVERT: A 82 MET cc_start: 0.7889 (ppp) cc_final: 0.7466 (ptp) REVERT: A 114 ARG cc_start: 0.7772 (mpt-90) cc_final: 0.7325 (mmm160) REVERT: C 798 LYS cc_start: 0.7326 (tttm) cc_final: 0.6768 (mptt) REVERT: C 805 LEU cc_start: 0.7403 (tt) cc_final: 0.6977 (mp) REVERT: C 811 ASP cc_start: 0.8291 (m-30) cc_final: 0.7630 (t0) REVERT: T 159 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7040 (ttmm) REVERT: T 315 LYS cc_start: 0.7028 (ttpt) cc_final: 0.6727 (ttpt) REVERT: T 357 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6822 (mtp85) outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 0.2811 time to fit residues: 67.2587 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 : 1.370 ------------------------------------------------------------------------------- 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 141 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 66 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.195302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141810 restraints weight = 12100.934| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.16 r_work: 0.3397 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12638 Z= 0.127 Angle : 0.526 8.440 17122 Z= 0.266 Chirality : 0.039 0.138 1928 Planarity : 0.004 0.051 2118 Dihedral : 12.397 168.642 1924 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.58 % Allowed : 7.08 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1481 helix: 2.23 (0.18), residues: 846 sheet: -0.30 (0.50), residues: 101 loop : -0.49 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 30 HIS 0.004 0.001 HIS C 583 PHE 0.024 0.001 PHE C 530 TYR 0.017 0.001 TYR 2 412 ARG 0.006 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 707) hydrogen bonds : angle 4.15544 ( 2043) covalent geometry : bond 0.00292 (12638) covalent geometry : angle 0.52597 (17122) *********************** 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 160 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (tp) REVERT: 2 155 MET cc_start: 0.6460 (tpt) cc_final: 0.6211 (tpt) REVERT: 2 222 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.5942 (mp) REVERT: 2 395 TYR cc_start: 0.8119 (m-10) cc_final: 0.7807 (m-10) REVERT: 2 434 THR cc_start: 0.8719 (m) cc_final: 0.8427 (t) REVERT: A 66 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7440 (mt) REVERT: A 82 MET cc_start: 0.7958 (ppp) cc_final: 0.7569 (ptp) REVERT: C 794 GLN cc_start: 0.6435 (mt0) cc_final: 0.6123 (mt0) REVERT: C 798 LYS cc_start: 0.7353 (tttm) cc_final: 0.6786 (mptt) REVERT: C 805 LEU cc_start: 0.7512 (tt) cc_final: 0.7122 (mp) REVERT: C 811 ASP cc_start: 0.8306 (m-30) cc_final: 0.7682 (t0) REVERT: C 842 MET cc_start: 0.6373 (mtp) cc_final: 0.5946 (mtp) REVERT: T 143 MET cc_start: 0.7174 (ttt) cc_final: 0.6754 (ttt) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 0.2586 time to fit residues: 59.9328 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 : 1.262 ------------------------------------------------------------------------------- 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 88 MET 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 141 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.192452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139815 restraints weight = 12054.654| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.23 r_work: 0.3368 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12638 Z= 0.144 Angle : 0.527 13.557 17122 Z= 0.267 Chirality : 0.039 0.142 1928 Planarity : 0.004 0.046 2118 Dihedral : 11.898 168.186 1924 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 1.66 % Allowed : 8.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1481 helix: 2.18 (0.18), residues: 853 sheet: -0.64 (0.50), residues: 100 loop : -0.47 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.018 0.001 PHE C 530 TYR 0.018 0.001 TYR 2 157 ARG 0.005 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 707) hydrogen bonds : angle 4.10154 ( 2043) covalent geometry : bond 0.00345 (12638) covalent geometry : angle 0.52665 (17122) *********************** 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 159 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.6485 (tpt) cc_final: 0.6252 (tpt) REVERT: 2 222 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.5974 (mp) REVERT: 2 395 TYR cc_start: 0.8165 (m-10) cc_final: 0.7863 (m-10) REVERT: A 66 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7497 (mt) REVERT: A 82 MET cc_start: 0.7954 (ppp) cc_final: 0.7594 (ptp) REVERT: C 438 MET cc_start: 0.3228 (ttp) cc_final: 0.3012 (mtp) REVERT: C 682 ASP cc_start: 0.8277 (t0) cc_final: 0.7537 (t70) REVERT: C 805 LEU cc_start: 0.7544 (tt) cc_final: 0.7170 (mp) REVERT: C 811 ASP cc_start: 0.8350 (m-30) cc_final: 0.7847 (t0) REVERT: C 842 MET cc_start: 0.6423 (mtp) cc_final: 0.5933 (mtp) REVERT: T 357 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6805 (mtp85) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 0.2696 time to fit residues: 61.9221 Evaluate side-chains 146 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain T residue 283 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 146 optimal weight: 0.0010 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 136 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- 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 794 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 = 0.4175 r_free = 0.4175 target = 0.197033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143226 restraints weight = 12107.238| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.06 r_work: 0.3404 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12638 Z= 0.102 Angle : 0.488 12.552 17122 Z= 0.247 Chirality : 0.038 0.131 1928 Planarity : 0.003 0.047 2118 Dihedral : 11.655 169.785 1924 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 10.02 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.22), residues: 1481 helix: 2.35 (0.18), residues: 853 sheet: -0.87 (0.47), residues: 115 loop : -0.31 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 30 HIS 0.005 0.001 HIS C 470 PHE 0.016 0.001 PHE C 530 TYR 0.017 0.001 TYR 2 412 ARG 0.005 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 707) hydrogen bonds : angle 3.97528 ( 2043) covalent geometry : bond 0.00223 (12638) covalent geometry : angle 0.48765 (17122) *********************** 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 157 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.845 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6456 (t80) REVERT: 2 155 MET cc_start: 0.6446 (tpt) cc_final: 0.6222 (tpt) REVERT: 2 222 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5984 (mp) REVERT: 2 395 TYR cc_start: 0.8144 (m-10) cc_final: 0.7855 (m-10) REVERT: A 66 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 82 MET cc_start: 0.7980 (ppp) cc_final: 0.7614 (ptp) REVERT: C 438 MET cc_start: 0.3241 (ttp) cc_final: 0.2983 (mtp) REVERT: C 682 ASP cc_start: 0.8130 (t0) cc_final: 0.7371 (t70) REVERT: C 695 GLN cc_start: 0.7575 (mt0) cc_final: 0.7334 (mt0) REVERT: C 797 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6316 (mt-10) REVERT: C 805 LEU cc_start: 0.7525 (tt) cc_final: 0.7164 (mp) REVERT: C 811 ASP cc_start: 0.8340 (m-30) cc_final: 0.7836 (t0) REVERT: T 357 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6863 (mtp85) outliers start: 19 outliers final: 10 residues processed: 149 average time/residue: 0.2705 time to fit residues: 61.2171 Evaluate side-chains 147 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 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 98 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 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 = 0.4166 r_free = 0.4166 target = 0.195986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142295 restraints weight = 12280.312| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.29 r_work: 0.3346 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12638 Z= 0.113 Angle : 0.493 13.437 17122 Z= 0.248 Chirality : 0.038 0.135 1928 Planarity : 0.003 0.044 2118 Dihedral : 11.444 169.245 1924 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 1.66 % Allowed : 10.55 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.22), residues: 1481 helix: 2.39 (0.18), residues: 853 sheet: -0.90 (0.47), residues: 115 loop : -0.28 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.013 0.001 PHE C 599 TYR 0.016 0.001 TYR 2 412 ARG 0.006 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 707) hydrogen bonds : angle 3.95160 ( 2043) covalent geometry : bond 0.00260 (12638) covalent geometry : angle 0.49301 (17122) *********************** 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 170 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6563 (t80) REVERT: 2 155 MET cc_start: 0.6368 (tpt) cc_final: 0.6152 (tpt) REVERT: 2 222 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.5994 (mp) REVERT: 2 395 TYR cc_start: 0.8097 (m-10) cc_final: 0.7810 (m-10) REVERT: A 50 ARG cc_start: 0.7623 (ttm110) cc_final: 0.7360 (ttm110) REVERT: A 82 MET cc_start: 0.7954 (ppp) cc_final: 0.7607 (ptp) REVERT: C 438 MET cc_start: 0.3238 (ttp) cc_final: 0.2773 (ttp) REVERT: C 682 ASP cc_start: 0.8214 (t0) cc_final: 0.7435 (t70) REVERT: C 695 GLN cc_start: 0.7554 (mt0) cc_final: 0.7296 (mt0) REVERT: C 797 GLU cc_start: 0.6563 (mt-10) cc_final: 0.6134 (mt-10) REVERT: C 805 LEU cc_start: 0.7511 (tt) cc_final: 0.7168 (mp) REVERT: C 811 ASP cc_start: 0.8371 (m-30) cc_final: 0.7845 (t0) REVERT: T 315 LYS cc_start: 0.7121 (ttpt) cc_final: 0.6757 (ttmt) REVERT: T 357 ARG cc_start: 0.7120 (mtp85) cc_final: 0.6811 (mtp85) outliers start: 22 outliers final: 13 residues processed: 160 average time/residue: 0.2140 time to fit residues: 52.3903 Evaluate side-chains 153 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 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 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 353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 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 = 0.4124 r_free = 0.4124 target = 0.191356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137079 restraints weight = 12239.013| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3286 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12638 Z= 0.180 Angle : 0.566 15.104 17122 Z= 0.286 Chirality : 0.041 0.163 1928 Planarity : 0.004 0.072 2118 Dihedral : 11.462 166.297 1924 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer: Outliers : 1.73 % Allowed : 11.38 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1481 helix: 2.16 (0.17), residues: 854 sheet: -0.70 (0.51), residues: 100 loop : -0.40 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 102 HIS 0.005 0.001 HIS 2 320 PHE 0.025 0.001 PHE C 599 TYR 0.019 0.001 TYR 2 67 ARG 0.005 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 707) hydrogen bonds : angle 4.10203 ( 2043) covalent geometry : bond 0.00440 (12638) covalent geometry : angle 0.56641 (17122) *********************** 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 167 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6495 (t80) REVERT: 2 155 MET cc_start: 0.6498 (tpt) cc_final: 0.6253 (tpt) REVERT: 2 222 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.5974 (mp) REVERT: 2 395 TYR cc_start: 0.8123 (m-10) cc_final: 0.7829 (m-10) REVERT: A 82 MET cc_start: 0.7957 (ppp) cc_final: 0.7616 (ptp) REVERT: C 438 MET cc_start: 0.3204 (ttp) cc_final: 0.2745 (ttp) REVERT: C 695 GLN cc_start: 0.7660 (mt0) cc_final: 0.7348 (mt0) REVERT: C 794 GLN cc_start: 0.6788 (mt0) cc_final: 0.6473 (mt0) REVERT: C 797 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6221 (mt-10) REVERT: C 798 LYS cc_start: 0.7388 (tttm) cc_final: 0.6815 (mptt) REVERT: C 805 LEU cc_start: 0.7576 (tt) cc_final: 0.7229 (mp) REVERT: C 811 ASP cc_start: 0.8399 (m-30) cc_final: 0.7896 (t0) REVERT: C 842 MET cc_start: 0.6541 (mtp) cc_final: 0.6037 (mtp) REVERT: T 357 ARG cc_start: 0.7218 (mtp85) cc_final: 0.6870 (mtp85) outliers start: 23 outliers final: 13 residues processed: 158 average time/residue: 0.2194 time to fit residues: 53.4984 Evaluate side-chains 156 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 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 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 38 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 80 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.193804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139947 restraints weight = 12275.223| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.13 r_work: 0.3363 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12638 Z= 0.122 Angle : 0.513 13.523 17122 Z= 0.260 Chirality : 0.039 0.133 1928 Planarity : 0.004 0.062 2118 Dihedral : 11.299 167.184 1924 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 1.58 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.22), residues: 1481 helix: 2.31 (0.17), residues: 848 sheet: -0.98 (0.47), residues: 115 loop : -0.32 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 PHE 0.022 0.001 PHE C 599 TYR 0.016 0.001 TYR 2 412 ARG 0.007 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 707) hydrogen bonds : angle 4.00387 ( 2043) covalent geometry : bond 0.00285 (12638) covalent geometry : angle 0.51253 (17122) *********************** 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 158 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6476 (t80) REVERT: 2 155 MET cc_start: 0.6463 (tpt) cc_final: 0.6235 (tpt) REVERT: 2 222 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.5910 (mp) REVERT: 2 395 TYR cc_start: 0.8136 (m-10) cc_final: 0.7811 (m-10) REVERT: A 82 MET cc_start: 0.7937 (ppp) cc_final: 0.7593 (ptp) REVERT: C 438 MET cc_start: 0.3273 (ttp) cc_final: 0.2810 (ttp) REVERT: C 682 ASP cc_start: 0.8423 (t0) cc_final: 0.7861 (t0) REVERT: C 695 GLN cc_start: 0.7590 (mt0) cc_final: 0.7299 (mt0) REVERT: C 797 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6056 (mt-10) REVERT: C 805 LEU cc_start: 0.7511 (tt) cc_final: 0.7182 (mp) REVERT: C 811 ASP cc_start: 0.8403 (m-30) cc_final: 0.7879 (t0) REVERT: T 357 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6820 (mtp85) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 0.2047 time to fit residues: 47.5534 Evaluate side-chains 149 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 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 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.194777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140839 restraints weight = 12120.911| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.32 r_work: 0.3377 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2474 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= 0.113 Angle : 0.505 14.789 17122 Z= 0.255 Chirality : 0.038 0.133 1928 Planarity : 0.004 0.059 2118 Dihedral : 11.120 167.522 1924 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1481 helix: 2.39 (0.17), residues: 852 sheet: -1.12 (0.46), residues: 117 loop : -0.28 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 102 HIS 0.004 0.001 HIS C 583 PHE 0.021 0.001 PHE C 599 TYR 0.017 0.001 TYR 2 412 ARG 0.007 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 707) hydrogen bonds : angle 3.94978 ( 2043) covalent geometry : bond 0.00258 (12638) covalent geometry : angle 0.50504 (17122) *********************** 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 156 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6513 (t80) REVERT: 2 155 MET cc_start: 0.6396 (tpt) cc_final: 0.6163 (tpt) REVERT: 2 222 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6020 (mp) REVERT: A 82 MET cc_start: 0.7954 (ppp) cc_final: 0.7595 (ptp) REVERT: C 438 MET cc_start: 0.3227 (ttp) cc_final: 0.2785 (ttp) REVERT: C 682 ASP cc_start: 0.8438 (t0) cc_final: 0.8136 (t0) REVERT: C 695 GLN cc_start: 0.7645 (mt0) cc_final: 0.7337 (mt0) REVERT: C 797 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6105 (mt-10) REVERT: C 805 LEU cc_start: 0.7549 (tt) cc_final: 0.7237 (mp) REVERT: C 811 ASP cc_start: 0.8454 (m-30) cc_final: 0.8013 (t0) REVERT: T 315 LYS cc_start: 0.7137 (ttpt) cc_final: 0.6769 (ttmt) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.2245 time to fit residues: 52.0194 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 : 1.278 ------------------------------------------------------------------------------- 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 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 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 66 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 139 optimal weight: 0.0170 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5622 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.195744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141609 restraints weight = 12077.104| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.42 r_work: 0.3387 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12638 Z= 0.108 Angle : 0.505 14.549 17122 Z= 0.254 Chirality : 0.038 0.134 1928 Planarity : 0.003 0.045 2118 Dihedral : 10.979 167.335 1924 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 1.28 % Allowed : 12.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.22), residues: 1481 helix: 2.46 (0.17), residues: 856 sheet: -1.14 (0.46), residues: 117 loop : -0.23 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 102 HIS 0.004 0.001 HIS C 470 PHE 0.020 0.001 PHE C 599 TYR 0.017 0.001 TYR 2 412 ARG 0.006 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 707) hydrogen bonds : angle 3.91495 ( 2043) covalent geometry : bond 0.00242 (12638) covalent geometry : angle 0.50530 (17122) ********************** 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 151 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6539 (t80) REVERT: 2 155 MET cc_start: 0.6403 (tpt) cc_final: 0.6133 (tpt) REVERT: 2 222 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.5981 (mp) REVERT: A 82 MET cc_start: 0.7986 (ppp) cc_final: 0.7603 (ptp) REVERT: C 438 MET cc_start: 0.3249 (ttp) cc_final: 0.2807 (ttp) REVERT: C 682 ASP cc_start: 0.8447 (t0) cc_final: 0.8174 (t0) REVERT: C 695 GLN cc_start: 0.7620 (mt0) cc_final: 0.7339 (mt0) REVERT: C 797 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6122 (mt-10) REVERT: C 805 LEU cc_start: 0.7545 (tt) cc_final: 0.7244 (mp) REVERT: C 811 ASP cc_start: 0.8467 (m-30) cc_final: 0.7861 (t0) outliers start: 17 outliers final: 12 residues processed: 144 average time/residue: 0.2415 time to fit residues: 56.3655 Evaluate side-chains 146 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 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 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** 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 = 0.4141 r_free = 0.4141 target = 0.193303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139373 restraints weight = 12256.711| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.12 r_work: 0.3340 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2582 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= 0.136 Angle : 0.535 14.812 17122 Z= 0.268 Chirality : 0.039 0.161 1928 Planarity : 0.004 0.063 2118 Dihedral : 11.044 165.604 1924 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 12.89 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1481 helix: 2.36 (0.17), residues: 852 sheet: -1.13 (0.46), residues: 117 loop : -0.30 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.020 0.001 PHE C 599 TYR 0.016 0.001 TYR 2 157 ARG 0.006 0.000 ARG A 50 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 707) hydrogen bonds : angle 3.98588 ( 2043) covalent geometry : bond 0.00322 (12638) covalent geometry : angle 0.53485 (17122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8223.23 seconds wall clock time: 147 minutes 19.24 seconds (8839.24 seconds total)