Starting phenix.real_space_refine on Wed Feb 4 14:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.map" model { file = "/net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sgm_54873/02_2026/9sgm_54873.cif" } resolution = 2.86 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= 0.000 sd= 0.018 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 Fe 2 7.16 5 S 38 5.16 5 C 7002 2.51 5 N 1878 2.21 5 O 2069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10989 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5426 Classifications: {'peptide': 717} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 46, 'TRANS': 670} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 5477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5477 Classifications: {'peptide': 717} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 670} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.25 Number of scatterers: 10989 At special positions: 0 Unit cell: (85.696, 97.232, 127.72, 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) Fe 2 26.01 S 38 16.00 O 2069 8.00 N 1878 7.00 C 7002 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 572.2 milliseconds 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 52.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.548A pdb=" N ASP A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.819A pdb=" N SER A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.731A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.834A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.535A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.567A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 271 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.649A pdb=" N TYR A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.979A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 3.548A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 removed outlier: 4.239A pdb=" N GLY A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 421' Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.901A pdb=" N SER A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.074A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.609A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 634 removed outlier: 3.898A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 693 through 701 removed outlier: 4.077A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.809A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.586A pdb=" N VAL B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.589A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 4.092A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.772A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 258 through 271 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.511A pdb=" N LEU B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.587A pdb=" N ALA B 291 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.714A pdb=" N ASP B 311 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.081A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 453 through 464 removed outlier: 3.570A pdb=" N SER B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.952A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.737A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 581 through 588 removed outlier: 4.529A pdb=" N VAL B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 634 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 692 through 701 removed outlier: 4.148A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.578A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 715 No H-bonds generated for 'chain 'B' and resid 713 through 715' Processing helix chain 'B' and resid 716 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA3, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA4, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA7, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA8, first strand: chain 'B' and resid 667 through 670 464 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 4617 1.39 - 1.56: 6606 1.56 - 1.72: 1 1.72 - 1.88: 72 1.88 - 2.05: 8 Bond restraints: 11304 Sorted by residual: bond pdb=" CB VAL B 503 " pdb=" CG2 VAL B 503 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CG PRO A 219 " pdb=" CD PRO A 219 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.30e+00 bond pdb=" C ASN A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.15e+00 bond pdb=" C ALA B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 1.334 1.357 -0.024 2.34e-02 1.83e+03 1.02e+00 bond pdb=" C ASN B 51 " pdb=" O ASN B 51 " ideal model delta sigma weight residual 1.235 1.239 -0.005 4.70e-03 4.53e+04 9.42e-01 ... (remaining 11299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 15298 2.50 - 5.00: 140 5.00 - 7.50: 13 7.50 - 9.99: 1 9.99 - 12.49: 4 Bond angle restraints: 15456 Sorted by residual: angle pdb=" CB MET A 126 " pdb=" CG MET A 126 " pdb=" SD MET A 126 " ideal model delta sigma weight residual 112.70 125.19 -12.49 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CB MET A 664 " pdb=" CG MET A 664 " pdb=" SD MET A 664 " ideal model delta sigma weight residual 112.70 123.99 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA PRO B 131 " pdb=" N PRO B 131 " pdb=" CD PRO B 131 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 angle pdb=" CB MET A 242 " pdb=" CG MET A 242 " pdb=" SD MET A 242 " ideal model delta sigma weight residual 112.70 123.26 -10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CA PRO A 219 " pdb=" N PRO A 219 " pdb=" CD PRO A 219 " ideal model delta sigma weight residual 112.00 107.09 4.91 1.40e+00 5.10e-01 1.23e+01 ... (remaining 15451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5787 17.18 - 34.36: 560 34.36 - 51.54: 139 51.54 - 68.73: 31 68.73 - 85.91: 15 Dihedral angle restraints: 6532 sinusoidal: 2499 harmonic: 4033 Sorted by residual: dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N PRO A 219 " pdb=" CA PRO A 219 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU B 217 " pdb=" C GLU B 217 " pdb=" N ASN B 218 " pdb=" CA ASN B 218 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET B 255 " pdb=" C MET B 255 " pdb=" N ALA B 256 " pdb=" CA ALA B 256 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1131 0.037 - 0.074: 368 0.074 - 0.111: 106 0.111 - 0.148: 20 0.148 - 0.185: 2 Chirality restraints: 1627 Sorted by residual: chirality pdb=" CA PRO B 131 " pdb=" N PRO B 131 " pdb=" C PRO B 131 " pdb=" CB PRO B 131 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CG LEU A 220 " pdb=" CB LEU A 220 " pdb=" CD1 LEU A 220 " pdb=" CD2 LEU A 220 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA MET B 255 " pdb=" N MET B 255 " pdb=" C MET B 255 " pdb=" CB MET B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 1624 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 218 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 219 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 130 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO B 131 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 229 " 0.015 2.00e-02 2.50e+03 2.03e-02 8.25e+00 pdb=" CG TYR B 229 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 229 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 229 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 229 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR B 229 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 229 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 229 " -0.000 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1057 2.74 - 3.28: 10921 3.28 - 3.82: 19159 3.82 - 4.36: 23469 4.36 - 4.90: 39968 Nonbonded interactions: 94574 Sorted by model distance: nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.200 3.040 nonbonded pdb=" NH1 ARG A 146 " pdb=" O MET A 296 " model vdw 2.206 3.120 nonbonded pdb=" OH TYR B 337 " pdb=" OG1 THR B 394 " model vdw 2.247 3.040 nonbonded pdb=" O TRP A 198 " pdb=" NH2 ARG A 209 " model vdw 2.266 3.120 nonbonded pdb=" O VAL A 267 " pdb=" OG1 THR A 271 " model vdw 2.274 3.040 ... (remaining 94569 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 153 or (resid 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 685 or (resid 686 \ and (name N or name CA or name C or name O or name CB )) or resid 687 through 80 \ 1)) selection = (chain 'B' and (resid 24 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 210 or (resid 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 21 \ 6 or (resid 217 and (name N or name CA or name C or name O or name CB )) or resi \ d 218 through 228 or (resid 229 and (name N or name CA or name C or name O or na \ me CB )) or resid 230 through 300 or (resid 301 and (name N or name CA or name C \ or name O or name CB )) or resid 302 through 344 or (resid 345 and (name N or n \ ame CA or name C or name O or name CB )) or resid 346 through 502 or (resid 503 \ and (name N or name CA or name C or name O or name CB )) or resid 504 through 51 \ 0 or (resid 511 and (name N or name CA or name C or name O or name CB )) or resi \ d 512 through 514 or (resid 515 through 516 and (name N or name CA or name C or \ name O or name CB )) or resid 517 through 525 or (resid 526 and (name N or name \ CA or name C or name O or name CB )) or resid 527 through 576 or (resid 577 and \ (name N or name CA or name C or name O or name CB )) or resid 578 through 581 or \ (resid 582 and (name N or name CA or name C or name O or name CB )) or resid 58 \ 3 through 589 or (resid 590 through 591 and (name N or name CA or name C or name \ O or name CB )) or resid 592 through 650 or (resid 651 and (name N or name CA o \ r name C or name O or name CB )) or resid 652 through 801)) } 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=0.00 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: 1.480 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.740 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.003 0.172 11306 Z= 0.124 Angle : 0.574 12.492 15456 Z= 0.278 Chirality : 0.040 0.185 1627 Planarity : 0.005 0.120 2035 Dihedral : 15.124 85.908 3972 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.01 % Rotamer: Outliers : 0.82 % Allowed : 15.95 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.22), residues: 1430 helix: 1.27 (0.23), residues: 556 sheet: 2.02 (1.07), residues: 20 loop : -1.31 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.044 0.001 TYR B 229 PHE 0.008 0.001 PHE A 332 TRP 0.040 0.001 TRP B 107 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00297 (11304) covalent geometry : angle 0.57401 (15456) hydrogen bonds : bond 0.17380 ( 464) hydrogen bonds : angle 5.09520 ( 1212) Misc. bond : bond 0.13095 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 108 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8775 (m-70) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.5378 time to fit residues: 43.0667 Evaluate side-chains 67 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain B residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN A 717 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.075584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.059098 restraints weight = 23022.211| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.69 r_work: 0.2557 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11306 Z= 0.227 Angle : 0.593 11.372 15456 Z= 0.295 Chirality : 0.043 0.154 1627 Planarity : 0.006 0.117 2035 Dihedral : 6.206 106.956 1567 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.62 % Favored : 95.03 % Rotamer: Outliers : 2.02 % Allowed : 14.12 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.37 (0.22), residues: 1430 helix: 0.95 (0.22), residues: 584 sheet: 1.96 (1.08), residues: 20 loop : -1.23 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.042 0.002 TYR B 229 PHE 0.009 0.001 PHE B 129 TRP 0.018 0.001 TRP B 107 HIS 0.006 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00549 (11304) covalent geometry : angle 0.59272 (15456) hydrogen bonds : bond 0.04631 ( 464) hydrogen bonds : angle 4.45992 ( 1212) Misc. bond : bond 0.03443 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.7997 (pm20) cc_final: 0.7679 (pm20) outliers start: 22 outliers final: 5 residues processed: 83 average time/residue: 0.5419 time to fit residues: 49.2715 Evaluate side-chains 68 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.078133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.061738 restraints weight = 23042.665| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.71 r_work: 0.2577 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11306 Z= 0.137 Angle : 0.540 9.533 15456 Z= 0.264 Chirality : 0.041 0.161 1627 Planarity : 0.005 0.114 2035 Dihedral : 5.218 70.423 1558 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.87 % Rotamer: Outliers : 2.02 % Allowed : 13.93 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.22), residues: 1430 helix: 1.06 (0.22), residues: 586 sheet: 2.12 (1.12), residues: 20 loop : -1.16 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.036 0.001 TYR B 229 PHE 0.008 0.001 PHE A 332 TRP 0.013 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00336 (11304) covalent geometry : angle 0.54006 (15456) hydrogen bonds : bond 0.03923 ( 464) hydrogen bonds : angle 4.28414 ( 1212) Misc. bond : bond 0.06818 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.7937 (pm20) cc_final: 0.7625 (pm20) outliers start: 22 outliers final: 7 residues processed: 85 average time/residue: 0.4905 time to fit residues: 45.8198 Evaluate side-chains 70 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 54 optimal weight: 0.0370 chunk 38 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.063256 restraints weight = 22790.981| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.73 r_work: 0.2647 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11306 Z= 0.099 Angle : 0.526 10.940 15456 Z= 0.251 Chirality : 0.040 0.169 1627 Planarity : 0.005 0.108 2035 Dihedral : 4.856 68.229 1558 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.71 % Favored : 96.01 % Rotamer: Outliers : 1.28 % Allowed : 15.12 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.22), residues: 1430 helix: 1.26 (0.22), residues: 584 sheet: 2.26 (1.08), residues: 20 loop : -1.08 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.025 0.001 TYR B 229 PHE 0.007 0.001 PHE A 332 TRP 0.013 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00235 (11304) covalent geometry : angle 0.52637 (15456) hydrogen bonds : bond 0.03378 ( 464) hydrogen bonds : angle 4.13759 ( 1212) Misc. bond : bond 0.10075 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8583 (t0) REVERT: A 315 ILE cc_start: 0.9181 (mm) cc_final: 0.8962 (mm) REVERT: A 376 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7431 (t) REVERT: B 229 TYR cc_start: 0.8060 (m-80) cc_final: 0.7801 (m-80) outliers start: 14 outliers final: 4 residues processed: 84 average time/residue: 0.5504 time to fit residues: 50.6474 Evaluate side-chains 74 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 0.0570 chunk 24 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.078420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.061967 restraints weight = 22866.810| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.71 r_work: 0.2617 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11306 Z= 0.114 Angle : 0.537 11.367 15456 Z= 0.255 Chirality : 0.040 0.150 1627 Planarity : 0.005 0.107 2035 Dihedral : 4.860 69.140 1558 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.71 % Favored : 96.01 % Rotamer: Outliers : 1.37 % Allowed : 15.12 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: 0.14 (0.22), residues: 1430 helix: 1.47 (0.22), residues: 572 sheet: 2.37 (1.05), residues: 20 loop : -0.99 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 693 TYR 0.018 0.001 TYR B 229 PHE 0.007 0.001 PHE A 332 TRP 0.010 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00280 (11304) covalent geometry : angle 0.53729 (15456) hydrogen bonds : bond 0.03424 ( 464) hydrogen bonds : angle 4.05564 ( 1212) Misc. bond : bond 0.08805 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 137 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8574 (t0) REVERT: A 315 ILE cc_start: 0.9141 (mm) cc_final: 0.8923 (mm) REVERT: A 376 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7665 (t) outliers start: 15 outliers final: 5 residues processed: 77 average time/residue: 0.5079 time to fit residues: 43.2284 Evaluate side-chains 77 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 47 optimal weight: 0.0370 chunk 123 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.079710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.063380 restraints weight = 22683.694| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.69 r_work: 0.2652 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 11306 Z= 0.104 Angle : 0.523 11.837 15456 Z= 0.247 Chirality : 0.040 0.167 1627 Planarity : 0.005 0.108 2035 Dihedral : 4.803 69.644 1558 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.85 % Favored : 95.87 % Rotamer: Outliers : 1.01 % Allowed : 15.40 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.22), residues: 1430 helix: 1.57 (0.22), residues: 572 sheet: 2.52 (1.07), residues: 20 loop : -0.92 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.025 0.001 TYR B 229 PHE 0.007 0.001 PHE A 332 TRP 0.012 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00255 (11304) covalent geometry : angle 0.52317 (15456) hydrogen bonds : bond 0.03277 ( 464) hydrogen bonds : angle 3.95344 ( 1212) Misc. bond : bond 0.10046 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.7629 (pm20) cc_final: 0.7415 (pm20) REVERT: A 315 ILE cc_start: 0.9075 (mm) cc_final: 0.8868 (mm) outliers start: 11 outliers final: 5 residues processed: 81 average time/residue: 0.4882 time to fit residues: 43.8320 Evaluate side-chains 74 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 530 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.061040 restraints weight = 22998.487| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.77 r_work: 0.2609 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11306 Z= 0.148 Angle : 0.550 11.151 15456 Z= 0.260 Chirality : 0.041 0.170 1627 Planarity : 0.005 0.103 2035 Dihedral : 4.922 71.882 1558 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.99 % Favored : 95.73 % Rotamer: Outliers : 1.01 % Allowed : 15.95 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.22), residues: 1430 helix: 1.45 (0.22), residues: 586 sheet: 2.43 (1.06), residues: 20 loop : -0.94 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.030 0.001 TYR B 229 PHE 0.006 0.001 PHE A 720 TRP 0.010 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00364 (11304) covalent geometry : angle 0.55039 (15456) hydrogen bonds : bond 0.03610 ( 464) hydrogen bonds : angle 3.97315 ( 1212) Misc. bond : bond 0.05749 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.7750 (pm20) cc_final: 0.7473 (pm20) REVERT: A 315 ILE cc_start: 0.9052 (mm) cc_final: 0.8807 (mm) REVERT: A 376 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7470 (t) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.5059 time to fit residues: 41.8111 Evaluate side-chains 77 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 138 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.064311 restraints weight = 22820.291| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.77 r_work: 0.2640 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 11306 Z= 0.099 Angle : 0.537 12.098 15456 Z= 0.249 Chirality : 0.039 0.177 1627 Planarity : 0.005 0.100 2035 Dihedral : 4.756 70.095 1558 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.06 % Favored : 95.66 % Rotamer: Outliers : 0.92 % Allowed : 15.95 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.22), residues: 1430 helix: 1.54 (0.21), residues: 584 sheet: 2.61 (1.08), residues: 20 loop : -0.87 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.022 0.001 TYR B 229 PHE 0.007 0.001 PHE A 332 TRP 0.012 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00243 (11304) covalent geometry : angle 0.53702 (15456) hydrogen bonds : bond 0.03160 ( 464) hydrogen bonds : angle 3.89218 ( 1212) Misc. bond : bond 0.09900 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8185 (p0) cc_final: 0.7302 (t0) REVERT: A 315 ILE cc_start: 0.9021 (mm) cc_final: 0.8771 (mm) REVERT: A 376 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7340 (t) REVERT: B 516 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8444 (ptmm) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.4993 time to fit residues: 43.9476 Evaluate side-chains 76 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 112 optimal weight: 0.0070 chunk 4 optimal weight: 0.0060 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.0030 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.065226 restraints weight = 22528.264| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.65 r_work: 0.2697 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 11306 Z= 0.091 Angle : 0.535 12.345 15456 Z= 0.246 Chirality : 0.039 0.180 1627 Planarity : 0.005 0.097 2035 Dihedral : 4.664 69.553 1558 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.34 % Favored : 95.45 % Rotamer: Outliers : 0.46 % Allowed : 17.14 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.22), residues: 1430 helix: 1.64 (0.22), residues: 584 sheet: 2.69 (1.09), residues: 20 loop : -0.80 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 418 TYR 0.011 0.001 TYR B 155 PHE 0.006 0.001 PHE A 332 TRP 0.043 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00218 (11304) covalent geometry : angle 0.53470 (15456) hydrogen bonds : bond 0.02998 ( 464) hydrogen bonds : angle 3.82290 ( 1212) Misc. bond : bond 0.11999 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8228 (p0) cc_final: 0.7432 (t0) REVERT: A 315 ILE cc_start: 0.8983 (mm) cc_final: 0.8739 (mm) REVERT: A 376 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7384 (t) outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.5441 time to fit residues: 47.8092 Evaluate side-chains 72 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.079036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.062857 restraints weight = 22888.807| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.65 r_work: 0.2640 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11306 Z= 0.148 Angle : 0.562 11.797 15456 Z= 0.265 Chirality : 0.041 0.180 1627 Planarity : 0.005 0.096 2035 Dihedral : 4.854 72.428 1558 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.92 % Favored : 95.87 % Rotamer: Outliers : 0.55 % Allowed : 17.60 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.22), residues: 1430 helix: 1.55 (0.21), residues: 588 sheet: 2.45 (1.10), residues: 20 loop : -0.76 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.046 0.001 TYR B 229 PHE 0.006 0.001 PHE B 724 TRP 0.041 0.001 TRP B 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00365 (11304) covalent geometry : angle 0.56153 (15456) hydrogen bonds : bond 0.03474 ( 464) hydrogen bonds : angle 3.86473 ( 1212) Misc. bond : bond 0.06240 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2860 Ramachandran restraints generated. 1430 Oldfield, 0 Emsley, 1430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 194 ASP cc_start: 0.8507 (t0) cc_final: 0.8306 (t0) REVERT: A 207 ASP cc_start: 0.8248 (p0) cc_final: 0.7444 (t0) REVERT: A 315 ILE cc_start: 0.8963 (mm) cc_final: 0.8715 (mm) REVERT: A 376 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7421 (t) REVERT: B 516 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8430 (ptmm) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.5224 time to fit residues: 43.4342 Evaluate side-chains 74 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 chunk 34 optimal weight: 0.0670 chunk 134 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.064528 restraints weight = 22747.526| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.64 r_work: 0.2657 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 11306 Z= 0.102 Angle : 0.554 12.218 15456 Z= 0.256 Chirality : 0.040 0.183 1627 Planarity : 0.005 0.092 2035 Dihedral : 4.719 70.830 1558 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.52 % Rotamer: Outliers : 0.64 % Allowed : 17.51 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.22), residues: 1430 helix: 1.62 (0.21), residues: 586 sheet: 2.56 (1.09), residues: 20 loop : -0.72 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.041 0.001 TYR B 229 PHE 0.006 0.001 PHE A 332 TRP 0.039 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00252 (11304) covalent geometry : angle 0.55439 (15456) hydrogen bonds : bond 0.03128 ( 464) hydrogen bonds : angle 3.81042 ( 1212) Misc. bond : bond 0.09812 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.64 seconds wall clock time: 43 minutes 28.72 seconds (2608.72 seconds total)