Starting phenix.real_space_refine on Fri Jul 3 02:55:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.map" model { file = "/net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9st9_55213/07_2026/9st9_55213.cif" } resolution = 3.1 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 44 5.16 5 C 7456 2.51 5 N 1880 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 703, 5567 Classifications: {'peptide': 703} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 703, 5567 Classifications: {'peptide': 703} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5737 Chain: "B" Number of atoms: 5531 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 698, 5521 Classifications: {'peptide': 698} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 664} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 698, 5521 Classifications: {'peptide': 698} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 664} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 5690 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.50 residue: pdb=" N AHIS B 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.50 Time building chain proxies: 4.51, per 1000 atoms: 0.40 Number of scatterers: 11286 At special positions: 0 Unit cell: (107.3, 79.92, 105.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 44 16.00 O 1898 8.00 N 1880 7.00 C 7456 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2538 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 5 sheets defined 78.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.622A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.960A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.656A pdb=" N LEU A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.645A pdb=" N GLN A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.811A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.623A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 545 through 554 removed outlier: 4.020A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.788A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.781A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.502A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.544A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 182 through 202 removed outlier: 3.508A pdb=" N ARG B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.669A pdb=" N THR B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 3.958A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 439 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 464 through 468 removed outlier: 3.750A pdb=" N PHE B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 468' Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 491 through 509 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.718A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 559 removed outlier: 4.267A pdb=" N GLU B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 559' Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.729A pdb=" N ILE B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.533A pdb=" N LEU B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.495A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.604A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.535A pdb=" N ILE B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 720 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.997A pdb=" N VAL A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.972A pdb=" N VAL B 40 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 313 764 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 5055 1.40 - 1.57: 6520 1.57 - 1.75: 0 1.75 - 1.93: 88 1.93 - 2.11: 12 Bond restraints: 11675 Sorted by residual: bond pdb=" C ASN A 223 " pdb=" N BHIS A 224 " ideal model delta sigma weight residual 1.326 1.247 0.079 1.12e-02 7.97e+03 4.93e+01 bond pdb=" C ASN B 223 " pdb=" N BHIS B 224 " ideal model delta sigma weight residual 1.329 1.406 -0.077 1.35e-02 5.49e+03 3.27e+01 bond pdb=" C3C HEM A 803 " pdb=" CAC HEM A 803 " ideal model delta sigma weight residual 1.544 1.469 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C3C HEM B 801 " pdb=" CAC HEM B 801 " ideal model delta sigma weight residual 1.544 1.471 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C3C HEM B 804 " pdb=" CAC HEM B 804 " ideal model delta sigma weight residual 1.544 1.471 0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 11670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 15478 1.76 - 3.52: 392 3.52 - 5.29: 97 5.29 - 7.05: 20 7.05 - 8.81: 3 Bond angle restraints: 15990 Sorted by residual: angle pdb=" N ARG B 481 " pdb=" CA ARG B 481 " pdb=" C ARG B 481 " ideal model delta sigma weight residual 113.12 107.52 5.60 1.25e+00 6.40e-01 2.01e+01 angle pdb=" CA VAL B 489 " pdb=" C VAL B 489 " pdb=" O VAL B 489 " ideal model delta sigma weight residual 121.97 118.03 3.94 9.80e-01 1.04e+00 1.62e+01 angle pdb=" N TRP B 483 " pdb=" CA TRP B 483 " pdb=" C TRP B 483 " ideal model delta sigma weight residual 111.40 107.05 4.35 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N TYR B 25 " pdb=" CA TYR B 25 " pdb=" C TYR B 25 " ideal model delta sigma weight residual 114.56 110.34 4.22 1.27e+00 6.20e-01 1.11e+01 angle pdb=" N TRP B 482 " pdb=" CA TRP B 482 " pdb=" C TRP B 482 " ideal model delta sigma weight residual 113.16 109.07 4.09 1.24e+00 6.50e-01 1.09e+01 ... (remaining 15985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5693 17.94 - 35.88: 580 35.88 - 53.82: 156 53.82 - 71.75: 27 71.75 - 89.69: 27 Dihedral angle restraints: 6483 sinusoidal: 2492 harmonic: 3991 Sorted by residual: dihedral pdb=" C2B HEM A 803 " pdb=" C3B HEM A 803 " pdb=" CAB HEM A 803 " pdb=" CBB HEM A 803 " ideal model delta sinusoidal sigma weight residual 0.00 81.18 -81.18 2 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" C2C HEM B 804 " pdb=" C3C HEM B 804 " pdb=" CAC HEM B 804 " pdb=" CBC HEM B 804 " ideal model delta sinusoidal sigma weight residual 0.00 -71.23 71.23 2 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual 0.00 -71.06 71.06 2 1.00e+01 1.00e-02 4.29e+01 ... (remaining 6480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1290 0.047 - 0.094: 315 0.094 - 0.141: 63 0.141 - 0.187: 5 0.187 - 0.234: 3 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA VAL B 489 " pdb=" N VAL B 489 " pdb=" C VAL B 489 " pdb=" CB VAL B 489 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE A 564 " pdb=" CA ILE A 564 " pdb=" CG1 ILE A 564 " pdb=" CG2 ILE A 564 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1673 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 487 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C LEU B 487 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 487 " 0.022 2.00e-02 2.50e+03 pdb=" N TRP B 488 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 341 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C THR B 341 " -0.045 2.00e-02 2.50e+03 pdb=" O THR B 341 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 342 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 477 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C MET B 477 " 0.039 2.00e-02 2.50e+03 pdb=" O MET B 477 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 478 " -0.013 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 10 2.44 - 3.05: 7546 3.05 - 3.67: 17410 3.67 - 4.28: 25558 4.28 - 4.90: 42741 Nonbonded interactions: 93265 Sorted by model distance: nonbonded pdb="FE FE B 803 " pdb=" O HOH B 901 " model vdw 1.825 3.000 nonbonded pdb=" NE2 HIS A 486 " pdb="FE FE A 804 " model vdw 1.949 3.080 nonbonded pdb="FE FE A 804 " pdb=" O HOH A 901 " model vdw 1.960 3.000 nonbonded pdb=" NE2 HIS B 486 " pdb="FE FE B 803 " model vdw 1.985 3.080 nonbonded pdb=" NE2 HIS B 631 " pdb="FE HEM B 804 " model vdw 2.402 3.080 ... (remaining 93260 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 223 or resid 225 through 245 or (resid 246 and \ (name N or name CA or name C or name O or name CB )) or resid 247 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 0 through 576 or (resid 577 and (name N or name CA or name C or name O or name C \ B )) or resid 578 through 802)) selection = (chain 'B' and (resid 24 through 223 or resid 225 through 438 or resid 465 throu \ gh 802)) } 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=0.50 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: 5.190 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.580 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.007 0.210 11679 Z= 0.312 Angle : 0.702 8.809 15990 Z= 0.365 Chirality : 0.042 0.234 1676 Planarity : 0.004 0.049 1996 Dihedral : 16.714 89.692 3945 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer: Outliers : 2.44 % Allowed : 16.65 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1399 helix: 2.03 (0.18), residues: 960 sheet: None (None), residues: 0 loop : -0.82 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 432 TYR 0.014 0.001 TYR A 30 PHE 0.021 0.001 PHE A 492 TRP 0.018 0.001 TRP A 338 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.31 (11675) covalent geometry : angle 0.70157 / 0.37 (15990) hydrogen bonds : bond 0.14461 / 10.10 ( 764) hydrogen bonds : angle 5.29725 / 3.76 ( 2211) Misc. bond : bond 0.07609 / 3.48 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.417 Fit side-chains REVERT: B 515 MET cc_start: 0.9183 (ttp) cc_final: 0.8958 (ttp) outliers start: 27 outliers final: 20 residues processed: 108 average time/residue: 0.0890 time to fit residues: 15.2093 Evaluate side-chains 98 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 640 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067551 restraints weight = 61536.393| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.84 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 11679 Z= 0.118 Angle : 0.610 15.021 15990 Z= 0.275 Chirality : 0.038 0.161 1676 Planarity : 0.004 0.046 1996 Dihedral : 8.206 85.346 1592 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.27 % Allowed : 17.56 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.10 (0.24), residues: 1399 helix: 2.32 (0.17), residues: 970 sheet: None (None), residues: 0 loop : -0.85 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.014 0.001 TYR B 652 PHE 0.019 0.001 PHE B 253 TRP 0.018 0.001 TRP A 338 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11675) covalent geometry : angle 0.61047 / 0.28 (15990) hydrogen bonds : bond 0.04523 / 3.10 ( 764) hydrogen bonds : angle 4.32553 / 3.08 ( 2211) Misc. bond : bond 0.08258 / 3.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.423 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.0769 time to fit residues: 13.3913 Evaluate side-chains 89 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067020 restraints weight = 59844.082| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.81 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 11679 Z= 0.122 Angle : 0.588 10.833 15990 Z= 0.269 Chirality : 0.039 0.154 1676 Planarity : 0.004 0.050 1996 Dihedral : 6.898 84.228 1566 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 2.17 % Allowed : 17.19 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.26 (0.24), residues: 1399 helix: 2.46 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -0.78 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.013 0.001 TYR B 652 PHE 0.011 0.001 PHE B 253 TRP 0.015 0.001 TRP B 338 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (11675) covalent geometry : angle 0.58846 / 0.27 (15990) hydrogen bonds : bond 0.04084 / 2.79 ( 764) hydrogen bonds : angle 4.15892 / 2.96 ( 2211) Misc. bond : bond 0.10145 / 5.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.442 Fit side-chains REVERT: A 734 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8039 (tpp) REVERT: B 527 PHE cc_start: 0.7838 (t80) cc_final: 0.7610 (t80) outliers start: 24 outliers final: 14 residues processed: 105 average time/residue: 0.0901 time to fit residues: 14.9521 Evaluate side-chains 98 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 11 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** 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 = 0.3341 r_free = 0.3341 target = 0.087793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.065938 restraints weight = 69840.626| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 5.21 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 11679 Z= 0.134 Angle : 0.609 13.458 15990 Z= 0.274 Chirality : 0.039 0.154 1676 Planarity : 0.004 0.046 1996 Dihedral : 6.882 87.175 1566 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.90 % Allowed : 17.19 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.33 (0.24), residues: 1399 helix: 2.51 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 654 TYR 0.015 0.001 TYR B 406 PHE 0.008 0.001 PHE B 635 TRP 0.016 0.001 TRP B 338 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.13 (11675) covalent geometry : angle 0.60883 / 0.27 (15990) hydrogen bonds : bond 0.04058 / 2.78 ( 764) hydrogen bonds : angle 4.10948 / 2.93 ( 2211) Misc. bond : bond 0.12173 / 6.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.287 Fit side-chains REVERT: A 734 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8016 (tpp) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.0795 time to fit residues: 12.8463 Evaluate side-chains 100 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** 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 = 0.3348 r_free = 0.3348 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067554 restraints weight = 56538.707| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.73 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 11679 Z= 0.117 Angle : 0.594 14.032 15990 Z= 0.267 Chirality : 0.039 0.154 1676 Planarity : 0.004 0.048 1996 Dihedral : 6.659 85.830 1562 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 1.90 % Allowed : 17.47 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.39 (0.24), residues: 1399 helix: 2.56 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 432 TYR 0.023 0.001 TYR B 406 PHE 0.023 0.001 PHE B 527 TRP 0.017 0.001 TRP B 338 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11675) covalent geometry : angle 0.59379 / 0.27 (15990) hydrogen bonds : bond 0.03860 / 2.64 ( 764) hydrogen bonds : angle 4.06424 / 2.89 ( 2211) Misc. bond : bond 0.09502 / 4.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.416 Fit side-chains REVERT: A 734 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8015 (tpp) outliers start: 21 outliers final: 17 residues processed: 105 average time/residue: 0.0689 time to fit residues: 11.9305 Evaluate side-chains 105 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.067062 restraints weight = 73064.983| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 5.34 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 11679 Z= 0.111 Angle : 0.596 15.133 15990 Z= 0.265 Chirality : 0.039 0.193 1676 Planarity : 0.003 0.047 1996 Dihedral : 6.599 85.396 1562 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 2.08 % Allowed : 17.56 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.44 (0.24), residues: 1399 helix: 2.60 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.014 0.001 TYR B 652 PHE 0.008 0.001 PHE A 194 TRP 0.017 0.001 TRP B 338 HIS 0.004 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (11675) covalent geometry : angle 0.59595 / 0.27 (15990) hydrogen bonds : bond 0.03713 / 2.54 ( 764) hydrogen bonds : angle 4.02177 / 2.86 ( 2211) Misc. bond : bond 0.08288 / 4.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.315 Fit side-chains REVERT: A 478 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 734 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8037 (tpp) REVERT: B 699 MET cc_start: 0.7864 (tpp) cc_final: 0.7600 (tpp) outliers start: 23 outliers final: 20 residues processed: 105 average time/residue: 0.0692 time to fit residues: 11.8062 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 121 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** 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 = 0.3333 r_free = 0.3333 target = 0.086980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.065230 restraints weight = 67271.172| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 5.21 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 11679 Z= 0.142 Angle : 0.625 16.007 15990 Z= 0.278 Chirality : 0.040 0.156 1676 Planarity : 0.004 0.050 1996 Dihedral : 6.699 87.507 1562 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 17.56 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.40 (0.24), residues: 1399 helix: 2.55 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.75 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.018 0.001 TYR A 406 PHE 0.022 0.001 PHE B 527 TRP 0.015 0.001 TRP B 251 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 (11675) covalent geometry : angle 0.62488 / 0.28 (15990) hydrogen bonds : bond 0.03998 / 2.74 ( 764) hydrogen bonds : angle 4.04635 / 2.88 ( 2211) Misc. bond : bond 0.13976 / 6.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.418 Fit side-chains REVERT: A 734 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8061 (tpp) outliers start: 24 outliers final: 21 residues processed: 106 average time/residue: 0.0673 time to fit residues: 11.6998 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** 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 = 0.3318 r_free = 0.3318 target = 0.086068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064825 restraints weight = 59446.520| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.91 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 11679 Z= 0.159 Angle : 0.650 16.386 15990 Z= 0.286 Chirality : 0.040 0.156 1676 Planarity : 0.004 0.049 1996 Dihedral : 6.751 88.902 1562 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.17 % Allowed : 17.83 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.41 (0.24), residues: 1399 helix: 2.55 (0.17), residues: 974 sheet: None (None), residues: 0 loop : -0.74 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 267 TYR 0.013 0.001 TYR B 652 PHE 0.009 0.001 PHE B 635 TRP 0.020 0.001 TRP A 582 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (11675) covalent geometry : angle 0.64962 / 0.29 (15990) hydrogen bonds : bond 0.04217 / 2.89 ( 764) hydrogen bonds : angle 4.07493 / 2.91 ( 2211) Misc. bond : bond 0.16520 / 8.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.424 Fit side-chains REVERT: A 734 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8046 (tpp) outliers start: 24 outliers final: 22 residues processed: 104 average time/residue: 0.0702 time to fit residues: 12.1474 Evaluate side-chains 109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.088086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067041 restraints weight = 52179.050| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.56 r_work: 0.2739 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 11679 Z= 0.109 Angle : 0.611 16.604 15990 Z= 0.270 Chirality : 0.039 0.155 1676 Planarity : 0.003 0.048 1996 Dihedral : 6.637 86.159 1562 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 18.01 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.47 (0.24), residues: 1399 helix: 2.60 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.019 0.001 TYR A 406 PHE 0.024 0.001 PHE B 527 TRP 0.020 0.001 TRP B 338 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (11675) covalent geometry : angle 0.61139 / 0.27 (15990) hydrogen bonds : bond 0.03765 / 2.57 ( 764) hydrogen bonds : angle 3.99729 / 2.85 ( 2211) Misc. bond : bond 0.08335 / 4.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.336 Fit side-chains REVERT: A 734 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8212 (tpp) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.0742 time to fit residues: 12.5049 Evaluate side-chains 108 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068593 restraints weight = 49349.210| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.36 r_work: 0.2775 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 11679 Z= 0.103 Angle : 0.604 16.971 15990 Z= 0.268 Chirality : 0.038 0.154 1676 Planarity : 0.003 0.048 1996 Dihedral : 6.572 83.727 1562 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.63 % Allowed : 18.46 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.54 (0.24), residues: 1399 helix: 2.64 (0.17), residues: 973 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 513 TYR 0.016 0.001 TYR A 406 PHE 0.008 0.001 PHE A 194 TRP 0.020 0.001 TRP B 338 HIS 0.004 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (11675) covalent geometry : angle 0.60421 / 0.27 (15990) hydrogen bonds : bond 0.03460 / 2.37 ( 764) hydrogen bonds : angle 3.96078 / 2.82 ( 2211) Misc. bond : bond 0.05960 / 2.96 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2798 Ramachandran restraints generated. 1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.317 Fit side-chains REVERT: A 93 MET cc_start: 0.8977 (mmt) cc_final: 0.8708 (mmm) REVERT: A 734 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8140 (tpp) REVERT: B 393 MET cc_start: 0.8872 (mmm) cc_final: 0.8651 (mtp) outliers start: 18 outliers final: 16 residues processed: 109 average time/residue: 0.0742 time to fit residues: 13.0075 Evaluate side-chains 107 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 306 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 120 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 136 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 24 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 537 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 = 0.3381 r_free = 0.3381 target = 0.089540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067827 restraints weight = 79958.836| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 5.52 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11679 Z= 0.100 Angle : 0.603 17.058 15990 Z= 0.266 Chirality : 0.038 0.180 1676 Planarity : 0.003 0.048 1996 Dihedral : 6.446 83.022 1560 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 18.55 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.57 (0.24), residues: 1399 helix: 2.68 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.68 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.012 0.001 TYR B 652 PHE 0.026 0.001 PHE B 527 TRP 0.020 0.001 TRP A 338 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (11675) covalent geometry : angle 0.60303 / 0.27 (15990) hydrogen bonds : bond 0.03358 / 2.30 ( 764) hydrogen bonds : angle 3.91756 / 2.79 ( 2211) Misc. bond : bond 0.04996 / 2.47 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.79 seconds wall clock time: 38 minutes 9.24 seconds (2289.24 seconds total)