Starting phenix.real_space_refine on Fri Oct 23 08:42:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ye0_72842/10_2026/9ye0_72842.map" } resolution = 2.88 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= 0.109 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5620 2.51 5 N 1608 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2262 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2262 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2262 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2262 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 2.13, per 1000 atoms: 0.24 Number of scatterers: 9048 At special positions: 0 Unit cell: (105.664, 105.664, 68.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1772 8.00 N 1608 7.00 C 5620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 368.9 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 58.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.875A pdb=" N CYS A 73 " --> pdb=" O ILE A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 82 through 97 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.611A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 546 through 561 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'B' and resid 13 through 26 Processing helix chain 'B' and resid 37 through 49 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.875A pdb=" N CYS B 73 " --> pdb=" O ILE B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 82 through 97 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.599A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 546 through 561 Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 37 through 49 Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.875A pdb=" N CYS C 73 " --> pdb=" O ILE C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 82 through 97 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 144 through 153 removed outlier: 3.617A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 446 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 546 through 561 Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.876A pdb=" N CYS D 73 " --> pdb=" O ILE D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 82 through 97 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.617A pdb=" N LEU D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 482 through 490 Processing helix chain 'D' and resid 503 through 518 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 546 through 561 Processing helix chain 'D' and resid 565 through 572 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 removed outlier: 8.150A pdb=" N ILE A 55 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 32 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 7 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 33 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 9 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 8 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU A 124 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 104 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 removed outlier: 6.927A pdb=" N VAL A 451 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE A 476 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 453 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 429 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 56 removed outlier: 8.150A pdb=" N ILE B 55 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 32 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 7 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE B 33 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 9 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 8 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU B 124 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 104 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 474 through 477 removed outlier: 6.928A pdb=" N VAL B 451 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B 476 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 453 " --> pdb=" O ILE B 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 56 removed outlier: 8.149A pdb=" N ILE C 55 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 32 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE C 7 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 33 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 9 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 8 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU C 124 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 104 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 474 through 477 removed outlier: 6.927A pdb=" N VAL C 451 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 476 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 453 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 429 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 54 through 56 removed outlier: 8.150A pdb=" N ILE D 55 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL D 32 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 7 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE D 33 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 9 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 8 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU D 124 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU D 104 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 474 through 477 removed outlier: 6.926A pdb=" N VAL D 451 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 476 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 453 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 429 " --> pdb=" O LEU D 498 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1437 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: 1.52 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3176 1.34 - 1.46: 1579 1.46 - 1.58: 4285 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9120 Sorted by residual: bond pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.41e-01 bond pdb=" CG1 ILE B 462 " pdb=" CD1 ILE B 462 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.29e-01 bond pdb=" CG1 ILE A 462 " pdb=" CD1 ILE A 462 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.29e-01 bond pdb=" CG1 ILE D 462 " pdb=" CD1 ILE D 462 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.29e-01 bond pdb=" CG1 ILE C 462 " pdb=" CD1 ILE C 462 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.29e-01 ... (remaining 9115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12201 1.60 - 3.20: 146 3.20 - 4.79: 17 4.79 - 6.39: 0 6.39 - 7.99: 4 Bond angle restraints: 12368 Sorted by residual: angle pdb=" CB MET C 538 " pdb=" CG MET C 538 " pdb=" SD MET C 538 " ideal model delta sigma weight residual 112.70 120.69 -7.99 3.00e+00 1.11e-01 7.09e+00 angle pdb=" CB MET A 538 " pdb=" CG MET A 538 " pdb=" SD MET A 538 " ideal model delta sigma weight residual 112.70 120.69 -7.99 3.00e+00 1.11e-01 7.09e+00 angle pdb=" CB MET B 538 " pdb=" CG MET B 538 " pdb=" SD MET B 538 " ideal model delta sigma weight residual 112.70 120.69 -7.99 3.00e+00 1.11e-01 7.09e+00 angle pdb=" CB MET D 538 " pdb=" CG MET D 538 " pdb=" SD MET D 538 " ideal model delta sigma weight residual 112.70 120.67 -7.97 3.00e+00 1.11e-01 7.05e+00 angle pdb=" CA ASP B 108 " pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 112.60 114.69 -2.09 1.00e+00 1.00e+00 4.35e+00 ... (remaining 12363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 5024 17.37 - 34.74: 518 34.74 - 52.11: 119 52.11 - 69.48: 15 69.48 - 86.85: 12 Dihedral angle restraints: 5688 sinusoidal: 2136 harmonic: 3552 Sorted by residual: dihedral pdb=" CA ASP B 108 " pdb=" C ASP B 108 " pdb=" N SER B 109 " pdb=" CA SER B 109 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CG ARG C 72 " pdb=" CD ARG C 72 " pdb=" NE ARG C 72 " pdb=" CZ ARG C 72 " ideal model delta sinusoidal sigma weight residual -90.00 -131.72 41.72 2 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG D 72 " pdb=" CD ARG D 72 " pdb=" NE ARG D 72 " pdb=" CZ ARG D 72 " ideal model delta sinusoidal sigma weight residual -90.00 -131.68 41.68 2 1.50e+01 4.44e-03 9.43e+00 ... (remaining 5685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 929 0.027 - 0.054: 404 0.054 - 0.081: 115 0.081 - 0.108: 63 0.108 - 0.135: 49 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA ILE C 476 " pdb=" N ILE C 476 " pdb=" C ILE C 476 " pdb=" CB ILE C 476 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE B 55 " pdb=" N ILE B 55 " pdb=" C ILE B 55 " pdb=" CB ILE B 55 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE B 476 " pdb=" N ILE B 476 " pdb=" C ILE B 476 " pdb=" CB ILE B 476 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1557 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 58 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CG ASP D 58 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP D 58 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP D 58 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 58 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CG ASP C 58 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP C 58 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP C 58 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 58 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" CG ASP A 58 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP A 58 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP A 58 " 0.009 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 4984 3.01 - 3.49: 9089 3.49 - 3.96: 14266 3.96 - 4.43: 16694 4.43 - 4.90: 26724 Nonbonded interactions: 71757 Sorted by model distance: nonbonded pdb=" N ASN B 565 " pdb=" OD1 ASN B 565 " model vdw 2.542 3.120 nonbonded pdb=" N ASN D 565 " pdb=" OD1 ASN D 565 " model vdw 2.542 3.120 nonbonded pdb=" N ASN A 565 " pdb=" OD1 ASN A 565 " model vdw 2.542 3.120 nonbonded pdb=" N ASN C 565 " pdb=" OD1 ASN C 565 " model vdw 2.543 3.120 nonbonded pdb=" N SER C 480 " pdb=" OG SER C 480 " model vdw 2.651 2.496 ... (remaining 71752 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 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 : 0.002 0.031 9120 Z= 0.092 Angle : 0.455 7.988 12368 Z= 0.243 Chirality : 0.041 0.135 1560 Planarity : 0.003 0.032 1616 Dihedral : 15.240 86.845 3352 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.78 % Allowed : 19.66 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.25), residues: 1208 helix: 2.32 (0.21), residues: 652 sheet: 1.27 (0.38), residues: 200 loop : -0.66 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 136 PHE 0.007 0.001 PHE C 550 HIS 0.001 0.000 HIS C 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 9120) covalent geometry : angle 0.45537 / 0.24 (12368) hydrogen bonds : bond 0.15654 / 11.10 ( 483) hydrogen bonds : angle 4.45210 / 3.14 ( 1437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.370 Fit side-chains REVERT: A 29 ASN cc_start: 0.7640 (m-40) cc_final: 0.7312 (m-40) REVERT: A 34 SER cc_start: 0.8818 (t) cc_final: 0.8573 (m) REVERT: A 72 ARG cc_start: 0.7249 (ptt180) cc_final: 0.7004 (ptt180) REVERT: A 132 GLU cc_start: 0.7927 (tt0) cc_final: 0.7662 (mt-10) REVERT: A 141 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 435 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 483 SER cc_start: 0.7297 (m) cc_final: 0.6865 (t) REVERT: B 29 ASN cc_start: 0.7654 (m-40) cc_final: 0.7321 (m-40) REVERT: B 34 SER cc_start: 0.8829 (t) cc_final: 0.8583 (m) REVERT: B 72 ARG cc_start: 0.7243 (ptt180) cc_final: 0.6996 (ptt180) REVERT: B 132 GLU cc_start: 0.7918 (tt0) cc_final: 0.7605 (mt-10) REVERT: B 141 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 435 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (mp) REVERT: B 483 SER cc_start: 0.7296 (m) cc_final: 0.6862 (t) REVERT: C 29 ASN cc_start: 0.7635 (m-40) cc_final: 0.7305 (m-40) REVERT: C 34 SER cc_start: 0.8843 (t) cc_final: 0.8587 (m) REVERT: C 72 ARG cc_start: 0.7242 (ptt180) cc_final: 0.6996 (ptt180) REVERT: C 132 GLU cc_start: 0.7907 (tt0) cc_final: 0.7646 (mt-10) REVERT: C 141 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 435 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 483 SER cc_start: 0.7332 (m) cc_final: 0.6910 (t) REVERT: D 29 ASN cc_start: 0.7650 (m-40) cc_final: 0.7323 (m-40) REVERT: D 34 SER cc_start: 0.8844 (t) cc_final: 0.8591 (m) REVERT: D 72 ARG cc_start: 0.7235 (ptt180) cc_final: 0.6990 (ptt180) REVERT: D 132 GLU cc_start: 0.7890 (tt0) cc_final: 0.7596 (mt-10) REVERT: D 141 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7797 (mt-10) REVERT: D 435 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8639 (mp) REVERT: D 483 SER cc_start: 0.7329 (m) cc_final: 0.6901 (t) outliers start: 18 outliers final: 0 residues processed: 144 average time/residue: 0.4567 time to fit residues: 71.1248 Evaluate side-chains 128 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 435 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 28 GLN A 566 ASN B 25 GLN B 28 GLN B 566 ASN C 25 GLN C 28 GLN C 566 ASN D 25 GLN D 28 GLN D 566 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.151339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121787 restraints weight = 9442.974| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.75 r_work: 0.3147 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9120 Z= 0.220 Angle : 0.580 6.332 12368 Z= 0.286 Chirality : 0.046 0.158 1560 Planarity : 0.004 0.033 1616 Dihedral : 4.389 24.123 1272 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.14 % Allowed : 16.40 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.25), residues: 1208 helix: 2.19 (0.20), residues: 664 sheet: 0.78 (0.40), residues: 180 loop : -0.48 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 PHE 0.012 0.002 PHE B 509 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.22 ( 9120) covalent geometry : angle 0.57982 / 0.29 (12368) hydrogen bonds : bond 0.04761 / 3.33 ( 483) hydrogen bonds : angle 3.66309 / 2.61 ( 1437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 144 time to evaluate : 0.372 Fit side-chains REVERT: A 29 ASN cc_start: 0.7511 (m-40) cc_final: 0.7173 (m-40) REVERT: A 34 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8558 (m) REVERT: A 117 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.6997 (mpp) REVERT: A 132 GLU cc_start: 0.7600 (tt0) cc_final: 0.7199 (mt-10) REVERT: A 141 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 482 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7220 (t0) REVERT: B 29 ASN cc_start: 0.7514 (m-40) cc_final: 0.7176 (m-40) REVERT: B 34 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8562 (m) REVERT: B 117 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.6970 (mpp) REVERT: B 132 GLU cc_start: 0.7599 (tt0) cc_final: 0.7216 (mt-10) REVERT: B 141 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 482 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7201 (t0) REVERT: C 29 ASN cc_start: 0.7485 (m-40) cc_final: 0.7146 (m-40) REVERT: C 34 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8548 (m) REVERT: C 132 GLU cc_start: 0.7581 (tt0) cc_final: 0.7175 (mt-10) REVERT: C 141 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 482 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7221 (t0) REVERT: D 29 ASN cc_start: 0.7500 (m-40) cc_final: 0.7162 (m-40) REVERT: D 34 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8543 (m) REVERT: D 132 GLU cc_start: 0.7593 (tt0) cc_final: 0.7192 (mt-10) REVERT: D 141 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 482 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7209 (t0) outliers start: 52 outliers final: 8 residues processed: 177 average time/residue: 0.4283 time to fit residues: 82.2827 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 482 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [119, 88, 42, 20, 31, 61, 50, 21, 12, 46, 58] chunk 119 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 28 GLN A 566 ASN B 25 GLN B 28 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 566 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.124040 restraints weight = 9366.154| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.73 r_work: 0.3180 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9120 Z= 0.123 Angle : 0.462 5.189 12368 Z= 0.230 Chirality : 0.042 0.139 1560 Planarity : 0.003 0.030 1616 Dihedral : 3.740 12.997 1264 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 6.32 % Allowed : 15.22 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1208 helix: 2.38 (0.20), residues: 664 sheet: 0.84 (0.40), residues: 180 loop : -0.38 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 136 PHE 0.005 0.001 PHE B 509 HIS 0.002 0.000 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 9120) covalent geometry : angle 0.46233 / 0.23 (12368) hydrogen bonds : bond 0.03683 / 2.57 ( 483) hydrogen bonds : angle 3.49582 / 2.49 ( 1437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 129 time to evaluate : 0.372 Fit side-chains REVERT: A 29 ASN cc_start: 0.7508 (m-40) cc_final: 0.7173 (m-40) REVERT: A 34 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 132 GLU cc_start: 0.7590 (tt0) cc_final: 0.7197 (mt-10) REVERT: A 435 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8478 (mp) REVERT: A 495 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7710 (mtp180) REVERT: B 29 ASN cc_start: 0.7498 (m-40) cc_final: 0.7164 (m-40) REVERT: B 34 SER cc_start: 0.8888 (OUTLIER) cc_final: 0.8565 (m) REVERT: B 108 ASP cc_start: 0.8390 (t0) cc_final: 0.8187 (t0) REVERT: B 110 LYS cc_start: 0.8189 (pttp) cc_final: 0.7855 (ptpt) REVERT: B 132 GLU cc_start: 0.7594 (tt0) cc_final: 0.7203 (mt-10) REVERT: B 141 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7887 (mt-10) REVERT: B 435 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8448 (mp) REVERT: C 29 ASN cc_start: 0.7494 (m-40) cc_final: 0.7158 (m-40) REVERT: C 34 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8545 (m) REVERT: C 117 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.6881 (mpp) REVERT: C 132 GLU cc_start: 0.7594 (tt0) cc_final: 0.7201 (mt-10) REVERT: C 435 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 495 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7716 (mtp180) REVERT: C 506 ASP cc_start: 0.8028 (m-30) cc_final: 0.7826 (m-30) REVERT: D 29 ASN cc_start: 0.7518 (m-40) cc_final: 0.7184 (m-40) REVERT: D 34 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8540 (m) REVERT: D 117 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6891 (mpp) REVERT: D 132 GLU cc_start: 0.7579 (tt0) cc_final: 0.7188 (mt-10) REVERT: D 435 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (mp) REVERT: D 495 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7717 (mtp180) outliers start: 64 outliers final: 11 residues processed: 179 average time/residue: 0.4022 time to fit residues: 78.6730 Evaluate side-chains 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 495 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [111, 112, 68, 28, 15, 104, 76, 75, 78, 71, 100] chunk 111 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 28 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 28 GLN C 566 ASN D 25 GLN D 28 GLN D 566 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.152686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122959 restraints weight = 9460.141| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.75 r_work: 0.3192 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9120 Z= 0.138 Angle : 0.481 6.404 12368 Z= 0.237 Chirality : 0.043 0.152 1560 Planarity : 0.003 0.030 1616 Dihedral : 3.720 13.145 1264 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.72 % Allowed : 15.71 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.25), residues: 1208 helix: 2.49 (0.20), residues: 664 sheet: 0.81 (0.40), residues: 180 loop : -0.44 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 136 PHE 0.007 0.002 PHE C 509 HIS 0.001 0.000 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 9120) covalent geometry : angle 0.48074 / 0.24 (12368) hydrogen bonds : bond 0.03666 / 2.55 ( 483) hydrogen bonds : angle 3.41926 / 2.43 ( 1437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 0.352 Fit side-chains REVERT: A 29 ASN cc_start: 0.7499 (m-40) cc_final: 0.7178 (m-40) REVERT: A 34 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 117 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.6854 (mpp) REVERT: A 132 GLU cc_start: 0.7568 (tt0) cc_final: 0.7160 (mt-10) REVERT: A 435 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 495 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7724 (mtp180) REVERT: B 29 ASN cc_start: 0.7492 (m-40) cc_final: 0.7166 (m-40) REVERT: B 34 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8562 (m) REVERT: B 117 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.6863 (mpp) REVERT: B 132 GLU cc_start: 0.7573 (tt0) cc_final: 0.7168 (mt-10) REVERT: B 141 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7845 (mt-10) REVERT: B 435 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 29 ASN cc_start: 0.7485 (m-40) cc_final: 0.7163 (m-40) REVERT: C 34 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8545 (m) REVERT: C 117 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.6866 (mpp) REVERT: C 132 GLU cc_start: 0.7565 (tt0) cc_final: 0.7156 (mt-10) REVERT: C 435 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8459 (mp) REVERT: C 495 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7712 (mtp180) REVERT: C 506 ASP cc_start: 0.7999 (m-30) cc_final: 0.7779 (m-30) REVERT: D 29 ASN cc_start: 0.7503 (m-40) cc_final: 0.7182 (m-40) REVERT: D 34 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 117 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.6844 (mpp) REVERT: D 132 GLU cc_start: 0.7562 (tt0) cc_final: 0.7154 (mt-10) REVERT: D 435 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8454 (mp) REVERT: D 495 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7716 (mtp180) outliers start: 68 outliers final: 9 residues processed: 185 average time/residue: 0.4402 time to fit residues: 88.1599 Evaluate side-chains 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 495 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [23, 92, 10, 65, 71, 50, 41, 63, 79, 18, 100] chunk 23 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 566 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124464 restraints weight = 9368.136| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.74 r_work: 0.3192 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9120 Z= 0.116 Angle : 0.452 5.518 12368 Z= 0.226 Chirality : 0.042 0.148 1560 Planarity : 0.003 0.034 1616 Dihedral : 3.653 12.721 1264 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.73 % Allowed : 17.09 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.25), residues: 1208 helix: 2.54 (0.21), residues: 664 sheet: 1.11 (0.40), residues: 176 loop : -0.43 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 136 PHE 0.005 0.001 PHE C 509 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9120) covalent geometry : angle 0.45237 / 0.23 (12368) hydrogen bonds : bond 0.03371 / 2.34 ( 483) hydrogen bonds : angle 3.49923 / 2.49 ( 1437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.317 Fit side-chains REVERT: A 29 ASN cc_start: 0.7474 (m-40) cc_final: 0.7144 (m-40) REVERT: A 34 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 117 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.6886 (mpp) REVERT: A 132 GLU cc_start: 0.7511 (tt0) cc_final: 0.7111 (mt-10) REVERT: A 435 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 29 ASN cc_start: 0.7463 (m-40) cc_final: 0.7134 (m-40) REVERT: B 34 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8555 (m) REVERT: B 117 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.6890 (mpp) REVERT: B 132 GLU cc_start: 0.7522 (tt0) cc_final: 0.7124 (mt-10) REVERT: B 141 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 435 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8412 (mp) REVERT: C 29 ASN cc_start: 0.7465 (m-40) cc_final: 0.7139 (m-40) REVERT: C 34 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8550 (m) REVERT: C 117 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6832 (mpp) REVERT: C 132 GLU cc_start: 0.7530 (tt0) cc_final: 0.7127 (mt-10) REVERT: C 435 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8423 (mp) REVERT: C 506 ASP cc_start: 0.7987 (m-30) cc_final: 0.7775 (m-30) REVERT: D 29 ASN cc_start: 0.7477 (m-40) cc_final: 0.7139 (m-40) REVERT: D 34 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 117 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.6916 (mpp) REVERT: D 132 GLU cc_start: 0.7524 (tt0) cc_final: 0.7118 (mt-10) REVERT: D 435 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (mp) REVERT: D 495 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7667 (mtp180) outliers start: 58 outliers final: 12 residues processed: 173 average time/residue: 0.4362 time to fit residues: 81.9948 Evaluate side-chains 151 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 495 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [54, 71, 83, 12, 43, 93, 49, 45, 90, 34, 15] chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 28 GLN A 566 ASN B 25 GLN B 28 GLN B 566 ASN C 25 GLN C 28 GLN C 566 ASN D 25 GLN D 566 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.152065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.122173 restraints weight = 9393.465| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.76 r_work: 0.3161 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.157 Angle : 0.506 6.385 12368 Z= 0.249 Chirality : 0.044 0.192 1560 Planarity : 0.003 0.033 1616 Dihedral : 3.782 13.470 1264 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.43 % Allowed : 17.59 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1208 helix: 2.43 (0.20), residues: 664 sheet: 0.75 (0.40), residues: 180 loop : -0.47 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 PHE 0.008 0.002 PHE B 509 HIS 0.002 0.000 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 9120) covalent geometry : angle 0.50567 / 0.25 (12368) hydrogen bonds : bond 0.03821 / 2.65 ( 483) hydrogen bonds : angle 3.52076 / 2.51 ( 1437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.453 Fit side-chains REVERT: A 29 ASN cc_start: 0.7519 (m-40) cc_final: 0.7189 (m-40) REVERT: A 34 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8569 (m) REVERT: A 117 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.6891 (mpp) REVERT: A 132 GLU cc_start: 0.7603 (tt0) cc_final: 0.7221 (mt-10) REVERT: A 435 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8497 (mp) REVERT: A 482 ASP cc_start: 0.7181 (t70) cc_final: 0.6541 (t0) REVERT: B 29 ASN cc_start: 0.7514 (m-40) cc_final: 0.7199 (m-40) REVERT: B 34 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8579 (m) REVERT: B 117 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.6872 (mpp) REVERT: B 132 GLU cc_start: 0.7570 (tt0) cc_final: 0.7183 (mt-10) REVERT: B 141 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 435 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8470 (mp) REVERT: B 482 ASP cc_start: 0.7184 (t70) cc_final: 0.6541 (t0) REVERT: C 29 ASN cc_start: 0.7511 (m-40) cc_final: 0.7183 (m-40) REVERT: C 34 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (m) REVERT: C 117 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.6895 (mpp) REVERT: C 132 GLU cc_start: 0.7607 (tt0) cc_final: 0.7255 (mt-10) REVERT: C 435 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 482 ASP cc_start: 0.7194 (t0) cc_final: 0.6557 (t0) REVERT: C 506 ASP cc_start: 0.8008 (m-30) cc_final: 0.7799 (m-30) REVERT: D 29 ASN cc_start: 0.7522 (m-40) cc_final: 0.7191 (m-40) REVERT: D 34 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8523 (m) REVERT: D 117 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.6905 (mpp) REVERT: D 132 GLU cc_start: 0.7602 (tt0) cc_final: 0.7249 (mt-10) REVERT: D 435 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8480 (mp) REVERT: D 482 ASP cc_start: 0.7167 (t0) cc_final: 0.6520 (t0) outliers start: 55 outliers final: 13 residues processed: 170 average time/residue: 0.4043 time to fit residues: 75.0064 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [47, 79, 24, 112, 68, 34, 2, 37, 56, 35, 33] chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 566 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.153458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.123879 restraints weight = 9423.689| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.74 r_work: 0.3181 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9120 Z= 0.129 Angle : 0.473 6.435 12368 Z= 0.233 Chirality : 0.043 0.187 1560 Planarity : 0.003 0.032 1616 Dihedral : 3.681 13.006 1264 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.23 % Allowed : 17.09 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.25), residues: 1208 helix: 2.55 (0.21), residues: 664 sheet: 0.80 (0.40), residues: 180 loop : -0.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 PHE 0.006 0.001 PHE C 509 HIS 0.001 0.000 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 9120) covalent geometry : angle 0.47264 / 0.23 (12368) hydrogen bonds : bond 0.03473 / 2.41 ( 483) hydrogen bonds : angle 3.44298 / 2.45 ( 1437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 135 time to evaluate : 0.349 Fit side-chains REVERT: A 29 ASN cc_start: 0.7492 (m-40) cc_final: 0.7156 (m-40) REVERT: A 34 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8558 (m) REVERT: A 117 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: A 132 GLU cc_start: 0.7490 (tt0) cc_final: 0.7094 (mt-10) REVERT: A 435 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 29 ASN cc_start: 0.7483 (m-40) cc_final: 0.7148 (m-40) REVERT: B 34 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8567 (m) REVERT: B 117 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.6868 (mpp) REVERT: B 132 GLU cc_start: 0.7502 (tt0) cc_final: 0.7119 (mt-10) REVERT: B 141 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 435 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 29 ASN cc_start: 0.7482 (m-40) cc_final: 0.7148 (m-40) REVERT: C 34 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8553 (m) REVERT: C 117 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6820 (mpp) REVERT: C 132 GLU cc_start: 0.7492 (tt0) cc_final: 0.7096 (mt-10) REVERT: C 435 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8436 (mp) REVERT: C 506 ASP cc_start: 0.7956 (m-30) cc_final: 0.7732 (m-30) REVERT: D 29 ASN cc_start: 0.7482 (m-40) cc_final: 0.7144 (m-40) REVERT: D 34 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 117 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.6917 (mpp) REVERT: D 132 GLU cc_start: 0.7506 (tt0) cc_final: 0.7109 (mt-10) REVERT: D 435 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8438 (mp) REVERT: D 495 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7701 (mtp180) outliers start: 63 outliers final: 16 residues processed: 182 average time/residue: 0.3779 time to fit residues: 75.3741 Evaluate side-chains 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 495 ARG Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [104, 41, 55, 101, 51, 4, 27, 61, 50, 53, 83] chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 0.0370 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 566 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.155672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.126087 restraints weight = 9352.498| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.74 r_work: 0.3224 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9120 Z= 0.098 Angle : 0.444 6.556 12368 Z= 0.223 Chirality : 0.042 0.160 1560 Planarity : 0.003 0.032 1616 Dihedral : 3.517 13.624 1264 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.25 % Allowed : 19.37 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1208 helix: 2.78 (0.21), residues: 664 sheet: 1.11 (0.41), residues: 176 loop : -0.34 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 PHE 0.005 0.001 PHE A 550 HIS 0.001 0.000 HIS C 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 9120) covalent geometry : angle 0.44446 / 0.22 (12368) hydrogen bonds : bond 0.03006 / 2.08 ( 483) hydrogen bonds : angle 3.41815 / 2.43 ( 1437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7515 (m-40) cc_final: 0.7182 (m-40) REVERT: A 34 SER cc_start: 0.8831 (t) cc_final: 0.8549 (m) REVERT: A 132 GLU cc_start: 0.7541 (tt0) cc_final: 0.7183 (mt-10) REVERT: A 435 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 482 ASP cc_start: 0.7138 (t70) cc_final: 0.6534 (t0) REVERT: B 29 ASN cc_start: 0.7509 (m-40) cc_final: 0.7177 (m-40) REVERT: B 34 SER cc_start: 0.8825 (t) cc_final: 0.8548 (m) REVERT: B 117 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.6883 (mpp) REVERT: B 132 GLU cc_start: 0.7534 (tt0) cc_final: 0.7131 (mt-10) REVERT: B 141 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7818 (mt-10) REVERT: B 435 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 482 ASP cc_start: 0.7128 (t70) cc_final: 0.6520 (t0) REVERT: C 29 ASN cc_start: 0.7502 (m-40) cc_final: 0.7174 (m-40) REVERT: C 34 SER cc_start: 0.8819 (t) cc_final: 0.8537 (m) REVERT: C 132 GLU cc_start: 0.7543 (tt0) cc_final: 0.7153 (mt-10) REVERT: C 435 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 482 ASP cc_start: 0.7147 (t70) cc_final: 0.6544 (t0) REVERT: D 29 ASN cc_start: 0.7528 (m-40) cc_final: 0.7190 (m-40) REVERT: D 34 SER cc_start: 0.8815 (t) cc_final: 0.8528 (m) REVERT: D 132 GLU cc_start: 0.7551 (tt0) cc_final: 0.7159 (mt-10) REVERT: D 435 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8459 (mp) REVERT: D 482 ASP cc_start: 0.7143 (t70) cc_final: 0.6530 (t0) outliers start: 43 outliers final: 9 residues processed: 186 average time/residue: 0.3860 time to fit residues: 78.3514 Evaluate side-chains 159 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [22, 42, 50, 9, 2, 81, 29, 88, 71, 70, 36] chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 449 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 449 GLN D 566 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.154749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126681 restraints weight = 9295.387| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.63 r_work: 0.3216 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9120 Z= 0.118 Angle : 0.465 7.035 12368 Z= 0.233 Chirality : 0.043 0.169 1560 Planarity : 0.003 0.032 1616 Dihedral : 3.587 13.603 1264 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.25 % Allowed : 20.36 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.25), residues: 1208 helix: 2.74 (0.21), residues: 664 sheet: 1.14 (0.41), residues: 176 loop : -0.38 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 PHE 0.006 0.001 PHE C 509 HIS 0.001 0.000 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9120) covalent geometry : angle 0.46530 / 0.23 (12368) hydrogen bonds : bond 0.03232 / 2.24 ( 483) hydrogen bonds : angle 3.37554 / 2.40 ( 1437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.362 Fit side-chains REVERT: A 29 ASN cc_start: 0.7585 (m-40) cc_final: 0.7255 (m-40) REVERT: A 34 SER cc_start: 0.8831 (t) cc_final: 0.8554 (m) REVERT: A 117 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.6977 (mpp) REVERT: A 132 GLU cc_start: 0.7668 (tt0) cc_final: 0.7309 (mt-10) REVERT: A 435 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 482 ASP cc_start: 0.7200 (t70) cc_final: 0.6637 (t0) REVERT: B 29 ASN cc_start: 0.7571 (m-40) cc_final: 0.7270 (m-40) REVERT: B 34 SER cc_start: 0.8816 (t) cc_final: 0.8540 (m) REVERT: B 117 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.6947 (mpp) REVERT: B 132 GLU cc_start: 0.7668 (tt0) cc_final: 0.7304 (mt-10) REVERT: B 141 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 435 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 29 ASN cc_start: 0.7592 (m-40) cc_final: 0.7262 (m-40) REVERT: C 34 SER cc_start: 0.8847 (t) cc_final: 0.8574 (m) REVERT: C 132 GLU cc_start: 0.7638 (tt0) cc_final: 0.7294 (mt-10) REVERT: C 435 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8535 (mp) REVERT: C 482 ASP cc_start: 0.7215 (t70) cc_final: 0.6648 (t0) REVERT: D 29 ASN cc_start: 0.7597 (m-40) cc_final: 0.7285 (m-40) REVERT: D 34 SER cc_start: 0.8858 (t) cc_final: 0.8591 (m) REVERT: D 132 GLU cc_start: 0.7658 (tt0) cc_final: 0.7310 (mt-10) REVERT: D 435 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (mp) REVERT: D 482 ASP cc_start: 0.7214 (t70) cc_final: 0.6642 (t0) outliers start: 43 outliers final: 18 residues processed: 172 average time/residue: 0.3926 time to fit residues: 73.8382 Evaluate side-chains 158 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [117, 81, 68, 91, 103, 24, 63, 85, 67, 0, 37] chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 566 ASN D 25 GLN D 449 GLN D 566 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.155448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127353 restraints weight = 9225.131| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.63 r_work: 0.3241 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9120 Z= 0.111 Angle : 0.458 7.297 12368 Z= 0.230 Chirality : 0.042 0.135 1560 Planarity : 0.003 0.032 1616 Dihedral : 3.593 14.474 1264 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.15 % Allowed : 20.55 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1208 helix: 2.80 (0.21), residues: 660 sheet: 1.16 (0.40), residues: 176 loop : -0.38 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 PHE 0.005 0.001 PHE C 509 HIS 0.001 0.000 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 9120) covalent geometry : angle 0.45791 / 0.23 (12368) hydrogen bonds : bond 0.03156 / 2.18 ( 483) hydrogen bonds : angle 3.37111 / 2.40 ( 1437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7579 (m-40) cc_final: 0.7249 (m-40) REVERT: A 34 SER cc_start: 0.8812 (t) cc_final: 0.8538 (m) REVERT: A 117 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.6945 (mpp) REVERT: A 132 GLU cc_start: 0.7641 (tt0) cc_final: 0.7277 (mt-10) REVERT: A 435 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 29 ASN cc_start: 0.7581 (m-40) cc_final: 0.7252 (m-40) REVERT: B 34 SER cc_start: 0.8804 (t) cc_final: 0.8535 (m) REVERT: B 108 ASP cc_start: 0.8538 (t0) cc_final: 0.8152 (t0) REVERT: B 117 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.6910 (mpp) REVERT: B 132 GLU cc_start: 0.7626 (tt0) cc_final: 0.7278 (mt-10) REVERT: B 141 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 435 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 29 ASN cc_start: 0.7573 (m-40) cc_final: 0.7245 (m-40) REVERT: C 34 SER cc_start: 0.8798 (t) cc_final: 0.8528 (m) REVERT: C 132 GLU cc_start: 0.7629 (tt0) cc_final: 0.7256 (mt-10) REVERT: C 435 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 29 ASN cc_start: 0.7591 (m-40) cc_final: 0.7280 (m-40) REVERT: D 34 SER cc_start: 0.8804 (t) cc_final: 0.8535 (m) REVERT: D 132 GLU cc_start: 0.7632 (tt0) cc_final: 0.7280 (mt-10) REVERT: D 435 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8532 (mp) outliers start: 42 outliers final: 18 residues processed: 172 average time/residue: 0.4144 time to fit residues: 77.6272 Evaluate side-chains 157 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 435 ILE Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 533 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [105, 60, 103, 70, 83, 44, 76, 90, 111, 23, 13] chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 28 GLN A 566 ASN B 25 GLN B 566 ASN C 25 GLN C 28 GLN C 449 GLN C 566 ASN D 25 GLN D 28 GLN D 566 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.154125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.124728 restraints weight = 9251.127| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.72 r_work: 0.3200 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9120 Z= 0.151 Angle : 0.508 7.241 12368 Z= 0.252 Chirality : 0.045 0.213 1560 Planarity : 0.003 0.032 1616 Dihedral : 3.766 13.683 1264 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.46 % Allowed : 20.95 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.25), residues: 1208 helix: 2.64 (0.21), residues: 660 sheet: 1.01 (0.41), residues: 176 loop : -0.45 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 PHE 0.008 0.002 PHE B 509 HIS 0.002 0.000 HIS A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 ( 9120) covalent geometry : angle 0.50796 / 0.25 (12368) hydrogen bonds : bond 0.03659 / 2.53 ( 483) hydrogen bonds : angle 3.40915 / 2.43 ( 1437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.80 seconds wall clock time: 51 minutes 29.84 seconds (3089.84 seconds total)