Starting phenix.real_space_refine on Fri Jul 3 04:00:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pp_56720/07_2026/28pp_56720.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pp_56720/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/28pp_56720/07_2026/28pp_56720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pp_56720/07_2026/28pp_56720.map" model { file = "/net/cci-nas-00/data/ceres_data/28pp_56720/07_2026/28pp_56720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pp_56720/07_2026/28pp_56720.cif" } 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-6108/lib/python3.11/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, 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: 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: 4.77, per 1000 atoms: 0.41 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: 1.06 Conformation dependent library (CDL) restraints added in 963.2 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: 0.38 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: 2.34 Time building geometry restraints manager: 1.41 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 3.000 nonbonded pdb="FE FE B 803 " pdb=" O HOH B 959 " model vdw 1.994 3.000 nonbonded pdb=" NE2 HIS A 486 " pdb="FE FE A 804 " model vdw 2.066 3.080 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.520 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 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 : 0.440 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: 0.6655 time to fit residues: 81.4118 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 : 0.471 ------------------------------------------------------------------------------- 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... A 737 GLN B 537 HIS B 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.063826 restraints weight = 57803.792| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.51 r_work: 0.2565 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 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 = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11667 Z= 0.137 Angle : 0.645 15.193 15976 Z= 0.303 Chirality : 0.039 0.160 1676 Planarity : 0.004 0.040 1994 Dihedral : 7.105 88.219 1565 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 2.63 % Allowed : 22.85 % 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: 1.80 (0.24), residues: 1399 helix: 2.01 (0.17), residues: 979 sheet: -1.39 (1.07), residues: 20 loop : -0.73 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 358 TYR 0.014 0.001 TYR B 406 PHE 0.012 0.001 PHE A 555 TRP 0.020 0.001 TRP B 338 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11663) covalent geometry : angle 0.64474 / 0.30 (15976) hydrogen bonds : bond 0.04480 / 3.05 ( 761) hydrogen bonds : angle 4.36833 / 3.18 ( 2208) Misc. bond : bond 0.09945 / 4.99 ( 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 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.467 Fit side-chains REVERT: A 477 MET cc_start: 0.8103 (tmm) cc_final: 0.7876 (tmm) REVERT: A 559 GLU cc_start: 0.7637 (mp0) cc_final: 0.7247 (mp0) REVERT: A 583 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8240 (mpp) REVERT: B 396 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8775 (p0) REVERT: B 697 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7737 (mp0) outliers start: 29 outliers final: 7 residues processed: 101 average time/residue: 0.5863 time to fit residues: 64.9818 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 : 0.452 ------------------------------------------------------------------------------- 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 583 MET 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 511 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.064745 restraints weight = 39560.396| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.78 r_work: 0.2596 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 11667 Z= 0.140 Angle : 0.619 10.860 15976 Z= 0.291 Chirality : 0.039 0.157 1676 Planarity : 0.004 0.039 1994 Dihedral : 6.949 89.466 1557 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.54 % Allowed : 23.75 % Favored : 74.71 % 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: 2.16 (0.24), residues: 1399 helix: 2.28 (0.17), residues: 975 sheet: -1.00 (1.14), residues: 20 loop : -0.56 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 267 TYR 0.009 0.001 TYR B 652 PHE 0.025 0.001 PHE A 19 TRP 0.020 0.001 TRP B 338 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (11663) covalent geometry : angle 0.61879 / 0.29 (15976) hydrogen bonds : bond 0.04233 / 2.90 ( 761) hydrogen bonds : angle 4.17987 / 3.04 ( 2208) Misc. bond : bond 0.11930 / 5.77 ( 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 93 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.477 Fit side-chains REVERT: A 358 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: A 477 MET cc_start: 0.8145 (tmm) cc_final: 0.7935 (tmm) REVERT: A 559 GLU cc_start: 0.7684 (mp0) cc_final: 0.7344 (mp0) REVERT: B 133 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8005 (t0) REVERT: B 358 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7973 (mtm-85) REVERT: B 396 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8770 (p0) REVERT: B 471 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8993 (ptp-110) outliers start: 17 outliers final: 8 residues processed: 90 average time/residue: 0.5713 time to fit residues: 56.4458 Evaluate side-chains 81 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 471 ARG Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 624 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: 2.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.063001 restraints weight = 46758.876| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.08 r_work: 0.2552 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 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 = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 11667 Z= 0.167 Angle : 0.633 11.800 15976 Z= 0.294 Chirality : 0.040 0.133 1676 Planarity : 0.004 0.038 1994 Dihedral : 6.948 89.133 1557 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 2.18 % Allowed : 22.76 % Favored : 75.07 % 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: 2.24 (0.24), residues: 1399 helix: 2.34 (0.17), residues: 974 sheet: -0.77 (1.17), residues: 20 loop : -0.56 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 358 TYR 0.010 0.001 TYR A 324 PHE 0.016 0.001 PHE B 527 TRP 0.019 0.001 TRP B 338 HIS 0.008 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (11663) covalent geometry : angle 0.63302 / 0.29 (15976) hydrogen bonds : bond 0.04440 / 3.04 ( 761) hydrogen bonds : angle 4.14808 / 3.01 ( 2208) Misc. bond : bond 0.14357 / 7.16 ( 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: 24 poor density : 74 time to evaluate : 0.461 Fit side-chains REVERT: A 358 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: A 559 GLU cc_start: 0.7712 (mp0) cc_final: 0.7276 (mp0) REVERT: B 358 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8113 (mtm-85) REVERT: B 396 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8827 (p0) REVERT: B 471 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (ptp-110) REVERT: B 477 MET cc_start: 0.8037 (tmm) cc_final: 0.7758 (tmm) outliers start: 24 outliers final: 13 residues processed: 96 average time/residue: 0.5994 time to fit residues: 62.9473 Evaluate side-chains 84 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 LEU 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 471 ARG Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 715 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.062693 restraints weight = 52580.075| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 4.33 r_work: 0.2529 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 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 = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 11667 Z= 0.151 Angle : 0.620 11.215 15976 Z= 0.287 Chirality : 0.039 0.140 1676 Planarity : 0.004 0.037 1994 Dihedral : 6.833 89.805 1557 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 23.21 % Favored : 74.80 % 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: 2.31 (0.24), residues: 1399 helix: 2.41 (0.17), residues: 970 sheet: -1.66 (1.54), residues: 10 loop : -0.54 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 579 TYR 0.009 0.001 TYR A 324 PHE 0.027 0.001 PHE A 19 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (11663) covalent geometry : angle 0.61963 / 0.29 (15976) hydrogen bonds : bond 0.04236 / 2.90 ( 761) hydrogen bonds : angle 4.08708 / 2.96 ( 2208) Misc. bond : bond 0.11835 / 5.86 ( 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 98 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.449 Fit side-chains REVERT: A 358 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: A 559 GLU cc_start: 0.7795 (mp0) cc_final: 0.7308 (mp0) REVERT: B 358 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8156 (mtm-85) REVERT: B 396 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8840 (p0) REVERT: B 471 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.9037 (ptp-110) outliers start: 22 outliers final: 13 residues processed: 95 average time/residue: 0.5643 time to fit residues: 58.9674 Evaluate side-chains 91 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU 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 123 LEU 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 471 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 0.0040 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.090317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.064575 restraints weight = 57779.209| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 4.56 r_work: 0.2561 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- 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 = 0.47 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 11667 Z= 0.114 Angle : 0.597 10.262 15976 Z= 0.275 Chirality : 0.038 0.130 1676 Planarity : 0.004 0.039 1994 Dihedral : 6.648 87.921 1557 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.45 % Allowed : 23.66 % 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: 2.45 (0.24), residues: 1399 helix: 2.54 (0.17), residues: 969 sheet: -1.60 (1.61), residues: 10 loop : -0.52 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.011 0.001 TYR A 406 PHE 0.019 0.001 PHE B 527 TRP 0.021 0.001 TRP A 338 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.11 (11663) covalent geometry : angle 0.59660 / 0.27 (15976) hydrogen bonds : bond 0.03733 / 2.57 ( 761) hydrogen bonds : angle 3.99238 / 2.89 ( 2208) Misc. bond : bond 0.05973 / 2.91 ( 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 102 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.460 Fit side-chains REVERT: A 358 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8243 (mtm-85) REVERT: A 559 GLU cc_start: 0.7821 (mp0) cc_final: 0.7213 (mp0) REVERT: B 44 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8168 (p0) REVERT: B 358 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8160 (mtm-85) REVERT: B 396 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8839 (p0) REVERT: B 477 MET cc_start: 0.8027 (tmm) cc_final: 0.7753 (tmm) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.5360 time to fit residues: 59.9732 Evaluate side-chains 91 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 434 ILE 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 396 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.065961 restraints weight = 56609.774| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.52 r_work: 0.2599 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11667 Z= 0.105 Angle : 0.589 12.352 15976 Z= 0.269 Chirality : 0.037 0.127 1676 Planarity : 0.004 0.037 1994 Dihedral : 6.514 84.712 1557 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 23.75 % Favored : 74.71 % 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: 2.60 (0.17), residues: 971 sheet: None (None), residues: 0 loop : -0.51 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 579 TYR 0.009 0.001 TYR A 156 PHE 0.029 0.001 PHE A 19 TRP 0.021 0.001 TRP A 338 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (11663) covalent geometry : angle 0.58888 / 0.27 (15976) hydrogen bonds : bond 0.03450 / 2.39 ( 761) hydrogen bonds : angle 3.92883 / 2.84 ( 2208) Misc. bond : bond 0.03165 / 1.46 ( 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 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.447 Fit side-chains REVERT: A 358 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: A 559 GLU cc_start: 0.7760 (mp0) cc_final: 0.7154 (mp0) REVERT: B 44 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8099 (p0) REVERT: B 133 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8051 (t0) REVERT: B 358 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8229 (mtm-85) REVERT: B 396 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8809 (p0) REVERT: B 610 MET cc_start: 0.8828 (mmm) cc_final: 0.8503 (mtm) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.5397 time to fit residues: 58.4277 Evaluate side-chains 93 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 434 ILE 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 396 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.066731 restraints weight = 36852.193| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.73 r_work: 0.2624 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 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 = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11667 Z= 0.115 Angle : 0.593 10.503 15976 Z= 0.273 Chirality : 0.038 0.239 1676 Planarity : 0.004 0.041 1994 Dihedral : 6.499 84.444 1557 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.72 % Allowed : 23.84 % Favored : 74.43 % 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: 2.56 (0.17), residues: 977 sheet: None (None), residues: 0 loop : -0.49 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 579 TYR 0.011 0.001 TYR B 638 PHE 0.020 0.001 PHE B 527 TRP 0.019 0.001 TRP A 338 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.11 (11663) covalent geometry : angle 0.59273 / 0.27 (15976) hydrogen bonds : bond 0.03572 / 2.47 ( 761) hydrogen bonds : angle 3.92806 / 2.84 ( 2208) Misc. bond : bond 0.05207 / 2.52 ( 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: 19 poor density : 83 time to evaluate : 0.478 Fit side-chains REVERT: A 358 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8270 (mtm-85) REVERT: A 559 GLU cc_start: 0.7880 (mp0) cc_final: 0.7202 (mp0) REVERT: B 44 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8108 (p0) REVERT: B 133 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8081 (t0) REVERT: B 358 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8206 (mtm-85) REVERT: B 396 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8814 (p0) REVERT: B 477 MET cc_start: 0.7963 (tmm) cc_final: 0.7745 (tmm) REVERT: B 610 MET cc_start: 0.8858 (mmm) cc_final: 0.8499 (mtm) outliers start: 19 outliers final: 11 residues processed: 102 average time/residue: 0.5433 time to fit residues: 61.0738 Evaluate side-chains 91 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 434 ILE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.089948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.065493 restraints weight = 34342.233| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.61 r_work: 0.2605 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 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 = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 11667 Z= 0.135 Angle : 0.622 12.020 15976 Z= 0.284 Chirality : 0.039 0.285 1676 Planarity : 0.004 0.042 1994 Dihedral : 6.396 84.753 1554 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.72 % Allowed : 23.93 % 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: 2.50 (0.24), residues: 1399 helix: 2.51 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.013 0.001 TYR B 638 PHE 0.028 0.001 PHE A 19 TRP 0.018 0.001 TRP B 251 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.13 (11663) covalent geometry : angle 0.62164 / 0.28 (15976) hydrogen bonds : bond 0.03853 / 2.65 ( 761) hydrogen bonds : angle 3.98568 / 2.89 ( 2208) Misc. bond : bond 0.08935 / 4.41 ( 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 97 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.456 Fit side-chains REVERT: A 358 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8226 (mtm-85) REVERT: A 559 GLU cc_start: 0.7842 (mp0) cc_final: 0.7162 (mp0) REVERT: A 591 MET cc_start: 0.8532 (mmm) cc_final: 0.8266 (mmp) REVERT: B 44 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8122 (p0) REVERT: B 133 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8109 (t0) REVERT: B 358 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: B 396 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8841 (p0) REVERT: B 477 MET cc_start: 0.7993 (tmm) cc_final: 0.7780 (tmm) REVERT: B 610 MET cc_start: 0.8850 (mmm) cc_final: 0.8512 (mtm) outliers start: 19 outliers final: 13 residues processed: 96 average time/residue: 0.5094 time to fit residues: 54.2027 Evaluate side-chains 93 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 732 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 112 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 107 optimal weight: 0.0770 chunk 104 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.089969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.064381 restraints weight = 54483.958| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.45 r_work: 0.2562 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 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 = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 11667 Z= 0.190 Angle : 0.860 59.196 15976 Z= 0.471 Chirality : 0.041 0.597 1676 Planarity : 0.004 0.043 1994 Dihedral : 6.401 84.753 1554 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.45 % Allowed : 24.30 % Favored : 74.25 % Cbeta Deviations : 0.08 % 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: 2.49 (0.24), residues: 1399 helix: 2.51 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 579 TYR 0.051 0.002 TYR A 406 PHE 0.017 0.001 PHE A 19 TRP 0.017 0.001 TRP B 251 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (11663) covalent geometry : angle 0.86043 / 0.47 (15976) hydrogen bonds : bond 0.03828 / 2.64 ( 761) hydrogen bonds : angle 3.99105 / 2.90 ( 2208) Misc. bond : bond 0.08889 / 4.39 ( 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 93 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.450 Fit side-chains REVERT: A 358 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8239 (mtm-85) REVERT: A 559 GLU cc_start: 0.7849 (mp0) cc_final: 0.7166 (mp0) REVERT: A 591 MET cc_start: 0.8508 (mmm) cc_final: 0.8254 (mmp) REVERT: B 44 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8127 (p0) REVERT: B 133 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8114 (t0) REVERT: B 358 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8212 (mtm-85) REVERT: B 396 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8856 (p0) REVERT: B 477 MET cc_start: 0.8045 (tmm) cc_final: 0.7828 (tmm) REVERT: B 610 MET cc_start: 0.8843 (mmm) cc_final: 0.8513 (mtm) outliers start: 16 outliers final: 12 residues processed: 93 average time/residue: 0.5139 time to fit residues: 52.9423 Evaluate side-chains 92 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 548 VAL Chi-restraints excluded: chain A residue 561 VAL 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 133 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 396 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.090011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.064844 restraints weight = 45826.077| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 4.11 r_work: 0.2579 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 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 = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 11667 Z= 0.190 Angle : 0.860 59.196 15976 Z= 0.471 Chirality : 0.041 0.597 1676 Planarity : 0.004 0.043 1994 Dihedral : 6.401 84.753 1554 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.36 % Allowed : 24.48 % Favored : 74.16 % Cbeta Deviations : 0.08 % 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: 2.49 (0.24), residues: 1399 helix: 2.51 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 579 TYR 0.051 0.002 TYR A 406 PHE 0.017 0.001 PHE A 19 TRP 0.017 0.001 TRP B 251 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (11663) covalent geometry : angle 0.86043 / 0.47 (15976) hydrogen bonds : bond 0.03828 / 2.64 ( 761) hydrogen bonds : angle 3.99105 / 2.90 ( 2208) Misc. bond : bond 0.08889 / 4.39 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.76 seconds wall clock time: 62 minutes 20.49 seconds (3740.49 seconds total)