Starting phenix.real_space_refine on Fri Jul 3 12:54:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwg_47243/07_2026/9dwg_47243.map" } resolution = 3.3 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= 0.003 sd= 1.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 19 5.16 5 C 8237 2.51 5 N 2692 2.21 5 O 3294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14535 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2569 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.14, per 1000 atoms: 0.22 Number of scatterers: 14535 At special positions: 0 Unit cell: (97.468, 149.919, 137.529, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 293 15.00 O 3294 8.00 N 2692 7.00 C 8237 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: 1.04 Conformation dependent library (CDL) restraints added in 342.4 milliseconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 69.5% alpha, 4.6% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.898A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.676A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.528A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.583A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.712A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.360A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.746A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.698A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.632A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.617A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 4.351A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.045A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.882A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.509A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.662A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 29 Processing helix chain 'L' and resid 32 through 48 Processing helix chain 'L' and resid 55 through 62 removed outlier: 3.545A pdb=" N ALA L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 80 Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 91 through 101 Processing helix chain 'L' and resid 107 through 117 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 129 through 132 Processing helix chain 'L' and resid 133 through 142 Processing helix chain 'L' and resid 142 through 147 Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 removed outlier: 4.308A pdb=" N VAL L 214 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.517A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 289 Processing helix chain 'L' and resid 315 through 323 removed outlier: 3.513A pdb=" N ILE L 323 " --> pdb=" O ILE L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.836A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.952A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.835A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 4.061A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.312A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 177 removed outlier: 6.601A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293 534 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1668 1.28 - 1.41: 4813 1.41 - 1.55: 8291 1.55 - 1.68: 586 1.68 - 1.82: 35 Bond restraints: 15393 Sorted by residual: bond pdb=" C TYR D 83 " pdb=" O TYR D 83 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.19e-02 7.06e+03 5.97e+01 bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.611 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C HIS D 82 " pdb=" N TYR D 83 " ideal model delta sigma weight residual 1.334 1.264 0.070 1.41e-02 5.03e+03 2.45e+01 bond pdb=" C TYR D 83 " pdb=" N ASN D 84 " ideal model delta sigma weight residual 1.333 1.252 0.081 1.73e-02 3.34e+03 2.18e+01 bond pdb=" C ARG A 131 " pdb=" O ARG A 131 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.38e-02 5.25e+03 1.87e+01 ... (remaining 15388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21087 2.09 - 4.19: 854 4.19 - 6.28: 66 6.28 - 8.38: 14 8.38 - 10.47: 9 Bond angle restraints: 22030 Sorted by residual: angle pdb=" N TYR D 40 " pdb=" CA TYR D 40 " pdb=" C TYR D 40 " ideal model delta sigma weight residual 111.11 121.58 -10.47 1.20e+00 6.94e-01 7.62e+01 angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 111.71 104.22 7.49 1.15e+00 7.56e-01 4.24e+01 angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 111.02 120.86 -9.84 1.52e+00 4.33e-01 4.19e+01 angle pdb=" C LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta sigma weight residual 110.81 101.56 9.25 1.60e+00 3.91e-01 3.34e+01 angle pdb=" O4' DA I 39 " pdb=" C4' DA I 39 " pdb=" C3' DA I 39 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.32e+01 ... (remaining 22025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 7122 35.40 - 70.81: 1382 70.81 - 106.21: 21 106.21 - 141.61: 1 141.61 - 177.01: 4 Dihedral angle restraints: 8530 sinusoidal: 5420 harmonic: 3110 Sorted by residual: dihedral pdb=" CD ARG D 33 " pdb=" NE ARG D 33 " pdb=" CZ ARG D 33 " pdb=" NH1 ARG D 33 " ideal model delta sinusoidal sigma weight residual 0.00 -75.64 75.64 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" C TYR D 83 " pdb=" N TYR D 83 " pdb=" CA TYR D 83 " pdb=" CB TYR D 83 " ideal model delta harmonic sigma weight residual -122.60 -109.49 -13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" C LYS A 122 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " ideal model delta harmonic sigma weight residual -122.60 -112.39 -10.21 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 8527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2439 0.126 - 0.251: 51 0.251 - 0.377: 2 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 2494 Sorted by residual: chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.34 2.96 -0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" P DA K 120 " pdb=" OP1 DA K 120 " pdb=" OP2 DA K 120 " pdb=" O5' DA K 120 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CB VAL E 46 " pdb=" CA VAL E 46 " pdb=" CG1 VAL E 46 " pdb=" CG2 VAL E 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2491 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 33 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.40e+02 pdb=" NE ARG D 33 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG D 33 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 33 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG D 33 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 25 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ASN B 25 " -0.073 2.00e-02 2.50e+03 pdb=" O ASN B 25 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE B 26 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 23 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ARG B 23 " 0.060 2.00e-02 2.50e+03 pdb=" O ARG B 23 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 24 " -0.021 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3032 2.79 - 3.32: 13012 3.32 - 3.85: 28584 3.85 - 4.37: 31555 4.37 - 4.90: 46144 Nonbonded interactions: 122327 Sorted by model distance: nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.298 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.300 3.040 nonbonded pdb=" O VAL L 29 " pdb=" NH2 ARG L 112 " model vdw 2.303 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.313 3.040 ... (remaining 122322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 123) selection = chain 'H' } 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: 23.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 15393 Z= 0.524 Angle : 0.882 10.473 22030 Z= 0.701 Chirality : 0.054 0.628 2494 Planarity : 0.013 0.481 1779 Dihedral : 26.774 177.014 6526 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.89 % Allowed : 1.11 % Favored : 98.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.04 (0.26), residues: 1054 helix: 1.14 (0.20), residues: 701 sheet: 0.71 (0.84), residues: 30 loop : -0.12 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 49 TYR 0.030 0.002 TYR L 322 PHE 0.016 0.002 PHE A 84 TRP 0.005 0.001 TRP L 325 HIS 0.011 0.002 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.52 (15393) covalent geometry : angle 0.88245 / 0.70 (22030) hydrogen bonds : bond 0.11718 / 7.66 ( 900) hydrogen bonds : angle 4.49393 / 3.20 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8565 (mm) cc_final: 0.8304 (mm) REVERT: A 120 MET cc_start: 0.9246 (mtm) cc_final: 0.8696 (mtm) REVERT: B 78 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8144 (ptt90) REVERT: C 92 GLU cc_start: 0.8890 (pp20) cc_final: 0.8285 (pp20) REVERT: D 35 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8314 (mt-10) REVERT: E 59 GLU cc_start: 0.7878 (pm20) cc_final: 0.7551 (pm20) REVERT: E 81 ASP cc_start: 0.8810 (t70) cc_final: 0.8349 (t70) REVERT: E 97 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8214 (tt0) REVERT: E 125 GLN cc_start: 0.8864 (mp10) cc_final: 0.8648 (mp10) REVERT: F 84 MET cc_start: 0.8857 (tpt) cc_final: 0.8476 (tpp) REVERT: F 88 TYR cc_start: 0.8753 (m-80) cc_final: 0.8506 (m-80) REVERT: G 36 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8913 (ttpt) REVERT: G 72 ASP cc_start: 0.9110 (m-30) cc_final: 0.8870 (t0) REVERT: G 90 ASP cc_start: 0.8854 (t70) cc_final: 0.7842 (t70) REVERT: G 104 GLN cc_start: 0.8603 (pm20) cc_final: 0.8270 (pm20) REVERT: H 68 ASP cc_start: 0.8992 (t0) cc_final: 0.8727 (t0) REVERT: H 84 ASN cc_start: 0.9188 (t0) cc_final: 0.8869 (t0) REVERT: L 217 GLN cc_start: 0.7217 (mt0) cc_final: 0.6975 (pp30) outliers start: 8 outliers final: 3 residues processed: 177 average time/residue: 0.1440 time to fit residues: 35.0864 Evaluate side-chains 129 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 116 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 40.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 113 HIS G 82 HIS H 82 HIS H 84 ASN L 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.095031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056000 restraints weight = 56022.755| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.43 r_work: 0.2836 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15393 Z= 0.242 Angle : 0.674 7.868 22030 Z= 0.385 Chirality : 0.045 0.294 2494 Planarity : 0.005 0.062 1779 Dihedral : 30.313 178.453 4400 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 10.30 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.29 (0.26), residues: 1054 helix: 1.42 (0.19), residues: 718 sheet: 0.78 (0.70), residues: 42 loop : -0.41 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.028 0.002 TYR B 88 PHE 0.019 0.002 PHE L 181 TRP 0.004 0.001 TRP L 325 HIS 0.008 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.24 (15393) covalent geometry : angle 0.67354 / 0.38 (22030) hydrogen bonds : bond 0.05057 / 3.37 ( 900) hydrogen bonds : angle 3.61146 / 2.59 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9205 (mtm) cc_final: 0.8814 (mtm) REVERT: A 131 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8974 (ttp-170) REVERT: B 25 ASN cc_start: 0.8626 (m110) cc_final: 0.8084 (m-40) REVERT: C 92 GLU cc_start: 0.8702 (pp20) cc_final: 0.8096 (pp20) REVERT: E 59 GLU cc_start: 0.7945 (pm20) cc_final: 0.7525 (pm20) REVERT: E 81 ASP cc_start: 0.8812 (t70) cc_final: 0.8357 (t70) REVERT: E 97 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8251 (tt0) REVERT: E 125 GLN cc_start: 0.8957 (mp10) cc_final: 0.8732 (mm-40) REVERT: F 88 TYR cc_start: 0.8728 (m-10) cc_final: 0.8522 (m-80) REVERT: G 72 ASP cc_start: 0.9245 (m-30) cc_final: 0.8995 (m-30) REVERT: G 90 ASP cc_start: 0.8440 (t70) cc_final: 0.8061 (t0) REVERT: G 92 GLU cc_start: 0.8628 (pm20) cc_final: 0.8404 (pm20) REVERT: H 68 ASP cc_start: 0.9014 (t0) cc_final: 0.8679 (t0) REVERT: H 84 ASN cc_start: 0.9003 (t0) cc_final: 0.8582 (t0) REVERT: H 86 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: L 158 MET cc_start: 0.5177 (ptp) cc_final: 0.4905 (ptt) outliers start: 17 outliers final: 11 residues processed: 144 average time/residue: 0.1472 time to fit residues: 30.2176 Evaluate side-chains 134 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 73 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 46 optimal weight: 0.0980 chunk 82 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS D 84 ASN E 39 HIS E 108 ASN F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.094466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055052 restraints weight = 56616.717| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.48 r_work: 0.2814 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15393 Z= 0.239 Angle : 0.649 7.839 22030 Z= 0.374 Chirality : 0.044 0.302 2494 Planarity : 0.005 0.054 1779 Dihedral : 30.359 179.896 4396 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.21 % Allowed : 12.18 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.44 (0.26), residues: 1054 helix: 1.58 (0.19), residues: 715 sheet: 1.00 (0.66), residues: 41 loop : -0.50 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.019 0.002 TYR L 322 PHE 0.014 0.002 PHE L 181 TRP 0.004 0.001 TRP L 325 HIS 0.007 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (15393) covalent geometry : angle 0.64862 / 0.37 (22030) hydrogen bonds : bond 0.04876 / 3.30 ( 900) hydrogen bonds : angle 3.48181 / 2.49 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9217 (mtm) cc_final: 0.8875 (mtm) REVERT: B 25 ASN cc_start: 0.8642 (m110) cc_final: 0.8162 (m-40) REVERT: C 92 GLU cc_start: 0.8697 (pp20) cc_final: 0.8169 (pp20) REVERT: D 93 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: E 59 GLU cc_start: 0.7907 (pm20) cc_final: 0.7004 (pm20) REVERT: E 60 LEU cc_start: 0.9017 (mt) cc_final: 0.8668 (tt) REVERT: E 81 ASP cc_start: 0.8783 (t70) cc_final: 0.8324 (t70) REVERT: E 97 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8286 (tt0) REVERT: H 68 ASP cc_start: 0.9029 (t0) cc_final: 0.8724 (t0) REVERT: H 76 GLU cc_start: 0.8962 (tp30) cc_final: 0.8721 (tp30) REVERT: H 83 TYR cc_start: 0.8313 (m-10) cc_final: 0.8058 (m-10) REVERT: H 84 ASN cc_start: 0.9005 (t0) cc_final: 0.8588 (t0) REVERT: H 86 ARG cc_start: 0.8254 (ttm-80) cc_final: 0.7835 (ttm-80) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.1367 time to fit residues: 27.5481 Evaluate side-chains 137 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 50.0000 chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.095074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056795 restraints weight = 56109.589| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.31 r_work: 0.2861 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15393 Z= 0.141 Angle : 0.580 6.275 22030 Z= 0.341 Chirality : 0.041 0.301 2494 Planarity : 0.004 0.042 1779 Dihedral : 30.324 178.784 4388 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.55 % Allowed : 13.95 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.77 (0.26), residues: 1054 helix: 1.86 (0.20), residues: 710 sheet: 1.13 (0.63), residues: 41 loop : -0.42 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 32 TYR 0.018 0.001 TYR B 88 PHE 0.010 0.001 PHE L 76 TRP 0.004 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15393) covalent geometry : angle 0.57967 / 0.34 (22030) hydrogen bonds : bond 0.04080 / 2.78 ( 900) hydrogen bonds : angle 3.19025 / 2.29 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9196 (mtm) cc_final: 0.8832 (mtm) REVERT: B 25 ASN cc_start: 0.8577 (m110) cc_final: 0.8073 (m-40) REVERT: C 92 GLU cc_start: 0.8677 (pp20) cc_final: 0.8216 (pp20) REVERT: E 59 GLU cc_start: 0.7962 (pm20) cc_final: 0.7251 (pm20) REVERT: E 81 ASP cc_start: 0.8782 (t70) cc_final: 0.8326 (t70) REVERT: E 97 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8301 (tt0) REVERT: E 107 THR cc_start: 0.9403 (m) cc_final: 0.9082 (t) REVERT: H 68 ASP cc_start: 0.8976 (t0) cc_final: 0.8541 (t0) REVERT: H 71 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8981 (tm-30) REVERT: H 84 ASN cc_start: 0.8979 (t0) cc_final: 0.8553 (t0) REVERT: H 86 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7830 (ttm-80) REVERT: L 158 MET cc_start: 0.4596 (ptt) cc_final: 0.4236 (ptt) outliers start: 23 outliers final: 13 residues processed: 149 average time/residue: 0.1273 time to fit residues: 28.1306 Evaluate side-chains 137 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 40.0000 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 117 optimal weight: 50.0000 chunk 105 optimal weight: 40.0000 chunk 95 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.093615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054382 restraints weight = 56140.533| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.47 r_work: 0.2789 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 15393 Z= 0.279 Angle : 0.691 8.732 22030 Z= 0.387 Chirality : 0.045 0.303 2494 Planarity : 0.005 0.043 1779 Dihedral : 30.457 179.220 4388 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.33 % Allowed : 14.95 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.53 (0.26), residues: 1054 helix: 1.64 (0.20), residues: 711 sheet: 0.96 (0.65), residues: 42 loop : -0.43 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 49 TYR 0.020 0.002 TYR D 40 PHE 0.016 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.28 (15393) covalent geometry : angle 0.69097 / 0.39 (22030) hydrogen bonds : bond 0.05240 / 3.53 ( 900) hydrogen bonds : angle 3.44711 / 2.47 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8670 (m110) cc_final: 0.8183 (m-40) REVERT: C 92 GLU cc_start: 0.8641 (pp20) cc_final: 0.8190 (pp20) REVERT: E 59 GLU cc_start: 0.8069 (pm20) cc_final: 0.7281 (pm20) REVERT: E 60 LEU cc_start: 0.8853 (tp) cc_final: 0.8351 (tt) REVERT: E 81 ASP cc_start: 0.8805 (t70) cc_final: 0.8343 (t70) REVERT: E 97 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8358 (tt0) REVERT: G 95 LYS cc_start: 0.9410 (tmmt) cc_final: 0.9199 (tttm) REVERT: H 68 ASP cc_start: 0.9056 (t0) cc_final: 0.8706 (t0) REVERT: H 83 TYR cc_start: 0.8357 (m-10) cc_final: 0.8055 (m-10) REVERT: H 84 ASN cc_start: 0.9095 (t0) cc_final: 0.8684 (t0) REVERT: H 86 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7916 (ttm-80) REVERT: L 158 MET cc_start: 0.4882 (ptt) cc_final: 0.3750 (ptt) outliers start: 21 outliers final: 18 residues processed: 128 average time/residue: 0.1252 time to fit residues: 23.0825 Evaluate side-chains 130 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056515 restraints weight = 55825.523| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.18 r_work: 0.2857 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15393 Z= 0.142 Angle : 0.583 6.115 22030 Z= 0.341 Chirality : 0.041 0.306 2494 Planarity : 0.004 0.043 1779 Dihedral : 30.368 179.161 4388 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.55 % Allowed : 15.95 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1054 helix: 1.88 (0.20), residues: 709 sheet: 1.12 (0.65), residues: 42 loop : -0.44 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.021 0.001 TYR D 40 PHE 0.010 0.001 PHE L 181 TRP 0.004 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (15393) covalent geometry : angle 0.58280 / 0.34 (22030) hydrogen bonds : bond 0.04057 / 2.76 ( 900) hydrogen bonds : angle 3.14774 / 2.25 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8892 (mtm) REVERT: B 25 ASN cc_start: 0.8545 (m110) cc_final: 0.8047 (m-40) REVERT: C 92 GLU cc_start: 0.8635 (pp20) cc_final: 0.8295 (pp20) REVERT: E 59 GLU cc_start: 0.7849 (pm20) cc_final: 0.7155 (pm20) REVERT: E 81 ASP cc_start: 0.8783 (t70) cc_final: 0.8323 (t70) REVERT: E 97 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8332 (tt0) REVERT: E 107 THR cc_start: 0.9429 (m) cc_final: 0.9122 (t) REVERT: H 68 ASP cc_start: 0.8974 (t0) cc_final: 0.8678 (t0) REVERT: H 84 ASN cc_start: 0.8996 (t0) cc_final: 0.8606 (t0) REVERT: H 86 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: L 158 MET cc_start: 0.4491 (ptt) cc_final: 0.3839 (ptt) REVERT: L 236 MET cc_start: 0.7098 (ptt) cc_final: 0.6874 (ttp) outliers start: 23 outliers final: 15 residues processed: 147 average time/residue: 0.1105 time to fit residues: 23.7004 Evaluate side-chains 135 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 74 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 118 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.094666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056477 restraints weight = 55939.916| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.40 r_work: 0.2834 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15393 Z= 0.142 Angle : 0.590 6.640 22030 Z= 0.341 Chirality : 0.041 0.302 2494 Planarity : 0.004 0.044 1779 Dihedral : 30.350 178.253 4388 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.66 % Allowed : 16.39 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.86 (0.26), residues: 1054 helix: 1.94 (0.20), residues: 710 sheet: 1.21 (0.66), residues: 42 loop : -0.42 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 42 TYR 0.017 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (15393) covalent geometry : angle 0.59014 / 0.34 (22030) hydrogen bonds : bond 0.04068 / 2.76 ( 900) hydrogen bonds : angle 3.11418 / 2.24 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8833 (mtm) REVERT: C 92 GLU cc_start: 0.8587 (pp20) cc_final: 0.8233 (pp20) REVERT: E 81 ASP cc_start: 0.8821 (t70) cc_final: 0.8350 (t70) REVERT: E 97 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8317 (tt0) REVERT: E 107 THR cc_start: 0.9407 (m) cc_final: 0.9093 (t) REVERT: H 68 ASP cc_start: 0.8951 (t0) cc_final: 0.8655 (t0) REVERT: H 83 TYR cc_start: 0.8225 (m-10) cc_final: 0.8018 (m-10) REVERT: H 84 ASN cc_start: 0.8997 (t0) cc_final: 0.8605 (t0) REVERT: H 86 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: L 236 MET cc_start: 0.7091 (ptt) cc_final: 0.6885 (ttp) outliers start: 24 outliers final: 20 residues processed: 143 average time/residue: 0.1236 time to fit residues: 25.7404 Evaluate side-chains 142 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 88 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.094217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055590 restraints weight = 55646.444| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.27 r_work: 0.2813 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15393 Z= 0.179 Angle : 0.623 10.206 22030 Z= 0.354 Chirality : 0.042 0.304 2494 Planarity : 0.004 0.043 1779 Dihedral : 30.379 178.643 4388 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.99 % Allowed : 16.50 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.91 (0.26), residues: 1054 helix: 1.93 (0.20), residues: 709 sheet: 1.45 (0.71), residues: 36 loop : -0.27 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 42 TYR 0.016 0.001 TYR D 40 PHE 0.010 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (15393) covalent geometry : angle 0.62285 / 0.35 (22030) hydrogen bonds : bond 0.04243 / 2.88 ( 900) hydrogen bonds : angle 3.20526 / 2.29 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8834 (mtm) REVERT: B 25 ASN cc_start: 0.8663 (m-40) cc_final: 0.8120 (m110) REVERT: C 92 GLU cc_start: 0.8579 (pp20) cc_final: 0.8330 (pm20) REVERT: C 111 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8881 (mm) REVERT: E 81 ASP cc_start: 0.8819 (t70) cc_final: 0.8339 (t70) REVERT: E 97 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8332 (tt0) REVERT: H 68 ASP cc_start: 0.8987 (t0) cc_final: 0.8676 (t0) REVERT: H 84 ASN cc_start: 0.8999 (t0) cc_final: 0.8616 (t0) REVERT: H 86 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7824 (ttm-80) REVERT: L 155 MET cc_start: -0.1809 (tmm) cc_final: -0.2718 (ppp) REVERT: L 158 MET cc_start: 0.4882 (ppp) cc_final: 0.4279 (ppp) REVERT: L 191 MET cc_start: 0.3342 (tpp) cc_final: 0.2348 (tpp) REVERT: L 236 MET cc_start: 0.7098 (ptt) cc_final: 0.6876 (ttp) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.1105 time to fit residues: 22.0499 Evaluate side-chains 135 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 125 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055583 restraints weight = 56122.211| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.37 r_work: 0.2823 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15393 Z= 0.170 Angle : 0.620 12.905 22030 Z= 0.352 Chirality : 0.042 0.306 2494 Planarity : 0.004 0.045 1779 Dihedral : 30.383 178.550 4388 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.66 % Allowed : 16.83 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.88 (0.26), residues: 1054 helix: 1.90 (0.20), residues: 711 sheet: 1.55 (0.70), residues: 36 loop : -0.29 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 42 TYR 0.017 0.001 TYR D 40 PHE 0.009 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (15393) covalent geometry : angle 0.61979 / 0.35 (22030) hydrogen bonds : bond 0.04199 / 2.86 ( 900) hydrogen bonds : angle 3.21110 / 2.30 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8818 (mtm) REVERT: B 25 ASN cc_start: 0.8645 (m-40) cc_final: 0.8114 (m110) REVERT: C 90 ASP cc_start: 0.8209 (t0) cc_final: 0.7574 (t0) REVERT: C 92 GLU cc_start: 0.8627 (pp20) cc_final: 0.8280 (pp20) REVERT: C 111 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8906 (mm) REVERT: E 81 ASP cc_start: 0.8819 (t70) cc_final: 0.8344 (t70) REVERT: E 97 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8339 (tt0) REVERT: H 68 ASP cc_start: 0.8977 (t0) cc_final: 0.8681 (t0) REVERT: H 84 ASN cc_start: 0.8958 (t0) cc_final: 0.8600 (t0) REVERT: H 86 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7847 (ttm-80) REVERT: L 155 MET cc_start: -0.1461 (tmm) cc_final: -0.2508 (ppp) REVERT: L 158 MET cc_start: 0.4927 (ppp) cc_final: 0.4259 (ppp) REVERT: L 191 MET cc_start: 0.3779 (tpp) cc_final: 0.2817 (tpp) REVERT: L 236 MET cc_start: 0.7036 (ptt) cc_final: 0.6829 (ttp) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.1135 time to fit residues: 22.4910 Evaluate side-chains 135 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 76 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.094341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.055847 restraints weight = 55811.131| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.42 r_work: 0.2836 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15393 Z= 0.149 Angle : 0.605 11.005 22030 Z= 0.346 Chirality : 0.041 0.305 2494 Planarity : 0.004 0.045 1779 Dihedral : 30.359 177.896 4388 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.99 % Allowed : 17.72 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.91 (0.26), residues: 1054 helix: 1.91 (0.20), residues: 711 sheet: 1.60 (0.71), residues: 36 loop : -0.26 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 42 TYR 0.048 0.002 TYR H 83 PHE 0.007 0.001 PHE E 67 TRP 0.004 0.001 TRP L 325 HIS 0.008 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15393) covalent geometry : angle 0.60460 / 0.35 (22030) hydrogen bonds : bond 0.04070 / 2.78 ( 900) hydrogen bonds : angle 3.18328 / 2.28 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8814 (mtm) REVERT: B 25 ASN cc_start: 0.8619 (m-40) cc_final: 0.8088 (m110) REVERT: C 90 ASP cc_start: 0.8197 (t0) cc_final: 0.7555 (t0) REVERT: C 92 GLU cc_start: 0.8585 (pp20) cc_final: 0.8251 (pp20) REVERT: C 111 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8913 (mm) REVERT: E 81 ASP cc_start: 0.8812 (t70) cc_final: 0.8335 (t70) REVERT: E 97 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8346 (tt0) REVERT: E 107 THR cc_start: 0.9408 (m) cc_final: 0.9077 (t) REVERT: F 88 TYR cc_start: 0.8519 (m-80) cc_final: 0.8202 (m-80) REVERT: H 68 ASP cc_start: 0.8965 (t0) cc_final: 0.8607 (t0) REVERT: H 84 ASN cc_start: 0.8956 (t0) cc_final: 0.8524 (t0) REVERT: L 155 MET cc_start: -0.1230 (tmm) cc_final: -0.2397 (ppp) REVERT: L 158 MET cc_start: 0.4965 (ppp) cc_final: 0.4358 (ppp) REVERT: L 191 MET cc_start: 0.3796 (tpp) cc_final: 0.2886 (tpp) REVERT: L 236 MET cc_start: 0.7062 (ptt) cc_final: 0.6860 (ttp) outliers start: 18 outliers final: 16 residues processed: 134 average time/residue: 0.1151 time to fit residues: 22.7526 Evaluate side-chains 137 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain L residue 213 GLN Chi-restraints excluded: chain L residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 84 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.093635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054907 restraints weight = 55359.539| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.25 r_work: 0.2817 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15393 Z= 0.208 Angle : 0.638 10.670 22030 Z= 0.360 Chirality : 0.043 0.308 2494 Planarity : 0.004 0.044 1779 Dihedral : 30.442 178.739 4388 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.44 % Allowed : 17.39 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1.81 (0.26), residues: 1054 helix: 1.83 (0.20), residues: 712 sheet: 1.58 (0.72), residues: 36 loop : -0.29 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 42 TYR 0.045 0.002 TYR H 83 PHE 0.012 0.001 PHE A 104 TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15393) covalent geometry : angle 0.63778 / 0.36 (22030) hydrogen bonds : bond 0.04550 / 3.08 ( 900) hydrogen bonds : angle 3.29446 / 2.36 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5254.69 seconds wall clock time: 90 minutes 15.17 seconds (5415.17 seconds total)