Starting phenix.real_space_refine on Thu Jun 4 09:06:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pp_56720/06_2026/28pp_56720.map" } resolution = 2.9 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= 0.010 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 7450 2.51 5 N 1874 2.21 5 O 2246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11622 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5571 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 703, 5561 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, 5561 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: 5731 Chain: "B" Number of atoms: 5525 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 698, 5515 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, 5515 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: 5684 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 224 " occ=0.52 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.48 residue: pdb=" N AHIS B 224 " occ=0.53 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.47 Time building chain proxies: 5.32, per 1000 atoms: 0.46 Number of scatterers: 11622 At special positions: 0 Unit cell: (114.7, 76.22, 108.04, 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 2246 8.00 N 1874 7.00 C 7450 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: 1.18 Conformation dependent library (CDL) restraints added in 835.1 milliseconds 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: 81 helices and 5 sheets defined 78.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 removed outlier: 3.609A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (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: 3.914A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.540A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.703A pdb=" N GLN A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 356 Proline residue: A 352 - end of helix removed outlier: 3.567A 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: 3.569A 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: 3.792A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.778A 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 603 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.531A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.264A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.702A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 4.661A 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 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 removed outlier: 3.560A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.570A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.975A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) 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: 3.538A pdb=" N HIS B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 254 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.509A 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: 3.601A 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: 3.781A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 486 removed outlier: 3.744A pdb=" N ILE B 484 " --> pdb=" O TRP B 480 " (cutoff:3.500A) 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 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.728A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.808A pdb=" N ILE B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.855A 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 581 through 585 removed outlier: 3.875A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.650A pdb=" N LEU B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.525A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.433A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.617A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.647A 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 698 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 removed outlier: 3.704A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.563A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (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: 6.838A pdb=" N VAL B 40 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (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 313 761 hydrogen bonds defined for protein. 2208 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: 1.98 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 4894 1.39 - 1.56: 6669 1.56 - 1.73: 0 1.73 - 1.90: 84 1.90 - 2.07: 16 Bond restraints: 11663 Sorted by residual: bond pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.22e-02 6.72e+03 6.67e+00 bond pdb=" C ASN B 214 " pdb=" N TRP B 215 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.07e-02 2.33e+03 5.99e+00 bond pdb=" N GLU B 121 " pdb=" CA GLU B 121 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.21e+00 bond pdb=" N ARG B 187 " pdb=" CA ARG B 187 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.95e+00 bond pdb=" N LEU B 119 " pdb=" CA LEU B 119 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.33e-02 5.65e+03 4.49e+00 ... (remaining 11658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 15855 3.50 - 7.01: 115 7.01 - 10.51: 4 10.51 - 14.02: 0 14.02 - 17.52: 2 Bond angle restraints: 15976 Sorted by residual: angle pdb=" C THR A 545 " pdb=" N THR A 546 " pdb=" CA THR A 546 " ideal model delta sigma weight residual 120.06 125.52 -5.46 1.19e+00 7.06e-01 2.11e+01 angle pdb=" N LEU B 123 " pdb=" CA LEU B 123 " pdb=" C LEU B 123 " ideal model delta sigma weight residual 111.07 106.57 4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" N ILE B 392 " pdb=" CA ILE B 392 " pdb=" C ILE B 392 " ideal model delta sigma weight residual 111.90 108.75 3.15 8.10e-01 1.52e+00 1.51e+01 angle pdb=" C ALA B 100 " pdb=" N ARG B 101 " pdb=" CA ARG B 101 " ideal model delta sigma weight residual 120.44 115.51 4.93 1.36e+00 5.41e-01 1.31e+01 angle pdb=" N LEU B 510 " pdb=" CA LEU B 510 " pdb=" C LEU B 510 " ideal model delta sigma weight residual 114.64 109.20 5.44 1.52e+00 4.33e-01 1.28e+01 ... (remaining 15971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5635 17.96 - 35.93: 615 35.93 - 53.89: 171 53.89 - 71.85: 33 71.85 - 89.82: 19 Dihedral angle restraints: 6473 sinusoidal: 2482 harmonic: 3991 Sorted by residual: dihedral pdb=" CA ALA B 174 " pdb=" C ALA B 174 " pdb=" N MET B 175 " pdb=" CA MET B 175 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU A 559 " pdb=" C GLU A 559 " pdb=" N VAL A 560 " pdb=" CA VAL A 560 " ideal model delta harmonic sigma weight residual -180.00 -160.14 -19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PRO A 81 " pdb=" C PRO A 81 " pdb=" N ASP A 82 " pdb=" CA ASP A 82 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1141 0.040 - 0.080: 414 0.080 - 0.121: 103 0.121 - 0.161: 16 0.161 - 0.201: 2 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA LEU B 123 " pdb=" N LEU B 123 " pdb=" C LEU B 123 " pdb=" CB LEU B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA THR B 546 " pdb=" N THR B 546 " pdb=" C THR B 546 " pdb=" CB THR B 546 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA GLU B 121 " pdb=" N GLU B 121 " pdb=" C GLU B 121 " pdb=" CB GLU B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1673 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.28e+00 pdb=" N PRO B 589 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 597 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.42e+00 pdb=" C ALA B 597 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA B 597 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE B 598 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 331 " 0.013 2.00e-02 2.50e+03 1.27e-02 2.41e+00 pdb=" CG HIS B 331 " -0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS B 331 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS B 331 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 331 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 331 " 0.004 2.00e-02 2.50e+03 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 104 2.54 - 3.13: 8899 3.13 - 3.72: 18874 3.72 - 4.31: 26481 4.31 - 4.90: 44686 Nonbonded interactions: 99044 Sorted by model distance: nonbonded pdb="FE FE A 804 " pdb=" O HOH A 951 " model vdw 1.955 2.260 nonbonded pdb="FE FE B 803 " pdb=" O HOH B 959 " model vdw 1.994 2.260 nonbonded pdb=" NE2 HIS A 486 " pdb="FE FE A 804 " model vdw 2.066 2.340 nonbonded pdb=" NH2 ARG A 101 " pdb=" OD1 ASP A 107 " model vdw 2.225 3.120 nonbonded pdb=" N GLY A 465 " pdb=" O HOH A 901 " model vdw 2.229 3.120 ... (remaining 99039 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 745)) selection = (chain 'B' and (resid 24 through 223 or resid 225 through 438 or resid 465 throu \ gh 745)) } 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=0.47 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: 4.670 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: 0.040 Set scattering table: 0.030 Process input model: 15.790 Find NCS groups from input model: 0.240 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 : 0.006 0.267 11667 Z= 0.225 Angle : 0.737 17.520 15976 Z= 0.388 Chirality : 0.044 0.201 1676 Planarity : 0.004 0.045 1994 Dihedral : 16.893 89.818 3935 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 1.72 % Allowed : 22.12 % Favored : 76.16 % 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: 1.02 (0.23), residues: 1399 helix: 1.47 (0.17), residues: 962 sheet: -0.56 (1.68), residues: 10 loop : -1.10 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 471 TYR 0.021 0.002 TYR B 127 PHE 0.019 0.002 PHE B 555 TRP 0.019 0.002 TRP B 426 HIS 0.013 0.002 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (11663) covalent geometry : angle 0.73740 / 0.39 (15976) hydrogen bonds : bond 0.15384 / 10.14 ( 761) hydrogen bonds : angle 5.69705 / 4.15 ( 2208) Misc. bond : bond 0.18716 / 9.38 ( 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 117 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 44 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8321 (p0) outliers start: 19 outliers final: 7 residues processed: 113 average time/residue: 0.6550 time to fit residues: 79.8013 Evaluate side-chains 80 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.063972 restraints weight = 56924.133| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 4.49 r_work: 0.2559 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 11667 Z= 0.137 Angle : 0.635 11.116 15976 Z= 0.304 Chirality : 0.039 0.161 1676 Planarity : 0.004 0.039 1994 Dihedral : 7.164 89.431 1565 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.36 % Allowed : 23.30 % Favored : 74.34 % 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: 1.78 (0.23), residues: 1399 helix: 2.00 (0.17), residues: 978 sheet: -1.42 (1.07), residues: 20 loop : -0.73 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 358 TYR 0.016 0.001 TYR B 406 PHE 0.012 0.001 PHE A 555 TRP 0.020 0.001 TRP B 338 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11663) covalent geometry : angle 0.63503 / 0.30 (15976) hydrogen bonds : bond 0.04506 / 3.07 ( 761) hydrogen bonds : angle 4.37710 / 3.19 ( 2208) Misc. bond : bond 0.10644 / 5.32 ( 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 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.429 Fit side-chains REVERT: A 477 MET cc_start: 0.8145 (tmm) cc_final: 0.7923 (tmm) REVERT: A 514 ARG cc_start: 0.6226 (tpt170) cc_final: 0.6023 (ttm-80) REVERT: A 559 GLU cc_start: 0.7610 (mp0) cc_final: 0.7212 (mp0) REVERT: B 396 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8764 (p0) REVERT: B 528 MET cc_start: 0.7977 (tpt) cc_final: 0.7748 (tpt) outliers start: 26 outliers final: 6 residues processed: 98 average time/residue: 0.5579 time to fit residues: 59.7115 Evaluate side-chains 78 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN B 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065787 restraints weight = 39668.617| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.81 r_work: 0.2615 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 11667 Z= 0.121 Angle : 0.604 10.273 15976 Z= 0.284 Chirality : 0.038 0.172 1676 Planarity : 0.004 0.039 1994 Dihedral : 6.912 89.496 1557 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.81 % Allowed : 23.66 % Favored : 74.52 % 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: 2.21 (0.24), residues: 1399 helix: 2.33 (0.17), residues: 972 sheet: -2.04 (1.56), residues: 10 loop : -0.58 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 358 TYR 0.011 0.001 TYR B 406 PHE 0.026 0.001 PHE A 19 TRP 0.020 0.001 TRP B 338 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (11663) covalent geometry : angle 0.60431 / 0.28 (15976) hydrogen bonds : bond 0.03966 / 2.73 ( 761) hydrogen bonds : angle 4.14274 / 3.01 ( 2208) Misc. bond : bond 0.07915 / 3.94 ( 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 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.459 Fit side-chains REVERT: A 358 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8247 (mtm-85) REVERT: A 559 GLU cc_start: 0.7681 (mp0) cc_final: 0.7306 (mp0) REVERT: B 133 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7982 (t0) REVERT: B 358 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: B 396 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8749 (p0) REVERT: B 471 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8991 (ptp-110) outliers start: 20 outliers final: 7 residues processed: 97 average time/residue: 0.6066 time to fit residues: 63.9466 Evaluate side-chains 79 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.065269 restraints weight = 46801.561| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.12 r_work: 0.2598 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 11667 Z= 0.123 Angle : 0.594 10.675 15976 Z= 0.277 Chirality : 0.038 0.130 1676 Planarity : 0.004 0.037 1994 Dihedral : 6.814 87.407 1557 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 1.72 % Allowed : 23.39 % Favored : 74.89 % 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: 2.38 (0.24), residues: 1399 helix: 2.48 (0.17), residues: 971 sheet: -1.80 (1.64), residues: 10 loop : -0.56 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 267 TYR 0.010 0.001 TYR B 78 PHE 0.010 0.001 PHE A 555 TRP 0.019 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 (11663) covalent geometry : angle 0.59390 / 0.28 (15976) hydrogen bonds : bond 0.03843 / 2.64 ( 761) hydrogen bonds : angle 4.04607 / 2.94 ( 2208) Misc. bond : bond 0.08176 / 4.08 ( 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 98 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.420 Fit side-chains REVERT: A 358 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: A 559 GLU cc_start: 0.7725 (mp0) cc_final: 0.7249 (mp0) REVERT: B 133 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 358 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8160 (mtm-85) REVERT: B 396 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8772 (p0) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.5760 time to fit residues: 59.6932 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 568 HIS A 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.062916 restraints weight = 52509.373| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 4.33 r_work: 0.2535 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 11667 Z= 0.159 Angle : 0.634 11.939 15976 Z= 0.292 Chirality : 0.039 0.138 1676 Planarity : 0.004 0.041 1994 Dihedral : 6.813 86.698 1557 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 2.18 % Allowed : 23.48 % Favored : 74.34 % 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: 2.47 (0.17), residues: 973 sheet: -1.60 (1.63), residues: 10 loop : -0.52 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 579 TYR 0.018 0.001 TYR A 406 PHE 0.029 0.001 PHE A 19 TRP 0.017 0.001 TRP A 338 HIS 0.008 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (11663) covalent geometry : angle 0.63379 / 0.29 (15976) hydrogen bonds : bond 0.04306 / 2.96 ( 761) hydrogen bonds : angle 4.08924 / 2.97 ( 2208) Misc. bond : bond 0.13790 / 6.88 ( 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 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.444 Fit side-chains REVERT: A 358 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: A 559 GLU cc_start: 0.7779 (mp0) cc_final: 0.7265 (mp0) REVERT: B 44 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8209 (p0) REVERT: B 358 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: B 697 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8680 (mp0) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 0.5739 time to fit residues: 60.8757 Evaluate side-chains 91 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 61 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.063577 restraints weight = 57900.017| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 4.57 r_work: 0.2549 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 11667 Z= 0.126 Angle : 0.608 11.831 15976 Z= 0.279 Chirality : 0.038 0.131 1676 Planarity : 0.004 0.036 1994 Dihedral : 6.672 87.099 1557 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 1.90 % Allowed : 23.75 % Favored : 74.34 % 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: 2.54 (0.17), residues: 973 sheet: -1.27 (1.65), residues: 10 loop : -0.53 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 579 TYR 0.011 0.001 TYR A 406 PHE 0.010 0.001 PHE A 635 TRP 0.019 0.001 TRP A 338 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11663) covalent geometry : angle 0.60795 / 0.28 (15976) hydrogen bonds : bond 0.03911 / 2.69 ( 761) hydrogen bonds : angle 4.00931 / 2.91 ( 2208) Misc. bond : bond 0.08084 / 4.02 ( 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 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.269 Fit side-chains REVERT: A 358 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8209 (mtm-85) REVERT: A 559 GLU cc_start: 0.7803 (mp0) cc_final: 0.7198 (mp0) REVERT: B 44 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8195 (p0) REVERT: B 358 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8215 (mtm-85) REVERT: B 396 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8842 (p0) REVERT: B 697 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8588 (mp0) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.5161 time to fit residues: 54.8203 Evaluate side-chains 92 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.064530 restraints weight = 56894.069| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.49 r_work: 0.2562 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 11667 Z= 0.120 Angle : 0.603 10.986 15976 Z= 0.276 Chirality : 0.038 0.216 1676 Planarity : 0.004 0.036 1994 Dihedral : 6.592 85.648 1557 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 2.18 % Allowed : 23.75 % Favored : 74.07 % 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: 2.55 (0.24), residues: 1399 helix: 2.59 (0.17), residues: 973 sheet: None (None), residues: 0 loop : -0.51 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 579 TYR 0.010 0.001 TYR B 78 PHE 0.030 0.001 PHE A 19 TRP 0.019 0.001 TRP B 338 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (11663) covalent geometry : angle 0.60264 / 0.28 (15976) hydrogen bonds : bond 0.03789 / 2.61 ( 761) hydrogen bonds : angle 3.97944 / 2.88 ( 2208) Misc. bond : bond 0.07353 / 3.65 ( 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 106 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.443 Fit side-chains REVERT: A 358 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: A 559 GLU cc_start: 0.7765 (mp0) cc_final: 0.7138 (mp0) REVERT: B 44 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8147 (p0) REVERT: B 133 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8065 (t0) REVERT: B 358 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8228 (mtm-85) REVERT: B 610 MET cc_start: 0.8870 (mmm) cc_final: 0.8508 (mtm) REVERT: B 697 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8570 (mp0) outliers start: 24 outliers final: 14 residues processed: 104 average time/residue: 0.5315 time to fit residues: 60.6864 Evaluate side-chains 94 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.065631 restraints weight = 36642.856| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.77 r_work: 0.2608 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11667 Z= 0.116 Angle : 0.602 11.345 15976 Z= 0.276 Chirality : 0.038 0.270 1676 Planarity : 0.004 0.042 1994 Dihedral : 6.561 85.294 1557 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 1.81 % Allowed : 23.93 % Favored : 74.25 % 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: 2.53 (0.24), residues: 1399 helix: 2.54 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -0.49 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.010 0.001 TYR B 78 PHE 0.022 0.001 PHE B 527 TRP 0.020 0.001 TRP A 251 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11663) covalent geometry : angle 0.60224 / 0.28 (15976) hydrogen bonds : bond 0.03690 / 2.54 ( 761) hydrogen bonds : angle 3.96829 / 2.88 ( 2208) Misc. bond : bond 0.06018 / 2.97 ( 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 102 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.459 Fit side-chains REVERT: A 358 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8202 (mtm-85) REVERT: A 559 GLU cc_start: 0.7774 (mp0) cc_final: 0.7112 (mp0) REVERT: B 44 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8135 (p0) REVERT: B 133 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8083 (t0) REVERT: B 358 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8214 (mtm-85) REVERT: B 396 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8827 (p0) REVERT: B 610 MET cc_start: 0.8861 (mmm) cc_final: 0.8517 (mtm) REVERT: B 697 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8527 (mp0) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 0.5111 time to fit residues: 56.2961 Evaluate side-chains 97 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 0.0010 chunk 43 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066077 restraints weight = 33959.966| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.66 r_work: 0.2620 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11667 Z= 0.112 Angle : 0.598 10.080 15976 Z= 0.274 Chirality : 0.038 0.268 1676 Planarity : 0.004 0.043 1994 Dihedral : 6.502 84.869 1556 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 24.12 % Favored : 74.25 % 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: 2.55 (0.24), residues: 1399 helix: 2.56 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.014 0.001 TYR A 406 PHE 0.029 0.001 PHE A 19 TRP 0.021 0.001 TRP A 251 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 (11663) covalent geometry : angle 0.59842 / 0.27 (15976) hydrogen bonds : bond 0.03622 / 2.50 ( 761) hydrogen bonds : angle 3.95206 / 2.87 ( 2208) Misc. bond : bond 0.05284 / 2.60 ( 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 100 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: A 559 GLU cc_start: 0.7804 (mp0) cc_final: 0.7140 (mp0) REVERT: B 44 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8125 (p0) REVERT: B 133 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8066 (t0) REVERT: B 358 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: B 396 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8823 (p0) REVERT: B 610 MET cc_start: 0.8859 (mmm) cc_final: 0.8516 (mtm) REVERT: B 697 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8507 (mp0) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 0.5252 time to fit residues: 57.2123 Evaluate side-chains 95 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 107 optimal weight: 0.0070 chunk 104 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.065237 restraints weight = 53819.471| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 4.50 r_work: 0.2581 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11667 Z= 0.114 Angle : 0.597 10.166 15976 Z= 0.275 Chirality : 0.038 0.256 1676 Planarity : 0.004 0.044 1994 Dihedral : 6.479 84.513 1556 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.54 % Allowed : 24.30 % Favored : 74.16 % 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: 2.55 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -0.49 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.015 0.001 TYR A 406 PHE 0.010 0.001 PHE A 635 TRP 0.023 0.001 TRP A 251 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.11 (11663) covalent geometry : angle 0.59743 / 0.27 (15976) hydrogen bonds : bond 0.03606 / 2.49 ( 761) hydrogen bonds : angle 3.94321 / 2.87 ( 2208) Misc. bond : bond 0.05271 / 2.59 ( 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 100 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.437 Fit side-chains REVERT: A 358 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8261 (mtm-85) REVERT: A 559 GLU cc_start: 0.7852 (mp0) cc_final: 0.7183 (mp0) REVERT: B 44 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 133 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8078 (t0) REVERT: B 358 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8240 (mtm-85) REVERT: B 396 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8836 (p0) REVERT: B 610 MET cc_start: 0.8862 (mmm) cc_final: 0.8522 (mtm) REVERT: B 697 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8520 (mp0) outliers start: 17 outliers final: 11 residues processed: 99 average time/residue: 0.5586 time to fit residues: 60.6005 Evaluate side-chains 94 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.062050 restraints weight = 46081.473| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 4.11 r_work: 0.2524 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.257 11667 Z= 0.204 Angle : 0.683 13.823 15976 Z= 0.313 Chirality : 0.041 0.249 1676 Planarity : 0.004 0.046 1994 Dihedral : 6.586 84.913 1554 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.72 % Allowed : 24.30 % Favored : 73.98 % 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: 2.44 (0.17), residues: 980 sheet: -0.89 (1.69), residues: 10 loop : -0.47 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 579 TYR 0.020 0.002 TYR A 406 PHE 0.028 0.001 PHE A 19 TRP 0.021 0.001 TRP B 251 HIS 0.011 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 (11663) covalent geometry : angle 0.68302 / 0.31 (15976) hydrogen bonds : bond 0.04743 / 3.25 ( 761) hydrogen bonds : angle 4.11980 / 2.99 ( 2208) Misc. bond : bond 0.18489 / 9.21 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.26 seconds wall clock time: 60 minutes 13.30 seconds (3613.30 seconds total)