Starting phenix.real_space_refine on Thu Jun 12 19:56:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_47243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_47243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_47243.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_47243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwg_47243/06_2025/9dwg_47243.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 11.07, per 1000 atoms: 0.76 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: 3.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.37 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: 5.76 Time building geometry restraints manager: 4.11 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: 21423 2.09 - 4.19: 520 4.19 - 6.28: 64 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=" C TYR D 83 " pdb=" CA TYR D 83 " pdb=" CB TYR D 83 " ideal model delta sigma weight residual 110.79 101.14 9.65 1.68e+00 3.54e-01 3.30e+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 - 0.124: 2447 0.124 - 0.247: 43 0.247 - 0.371: 2 0.371 - 0.495: 0 0.495 - 0.618: 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 2.35 2.96 -0.62 2.00e-01 2.50e+01 9.56e+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 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.35e+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: 95.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.870 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.005 0.131 15393 Z= 0.277 Angle : 0.766 10.473 22030 Z= 0.453 Chirality : 0.047 0.618 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP L 325 HIS 0.011 0.002 HIS L 135 PHE 0.016 0.002 PHE A 84 TYR 0.030 0.002 TYR L 322 ARG 0.018 0.001 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.11718 ( 900) hydrogen bonds : angle 4.49393 ( 2295) covalent geometry : bond 0.00540 (15393) covalent geometry : angle 0.76568 (22030) *********************** 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 : 1.074 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: 0.8507 (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: 0.3189 time to fit residues: 77.3642 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 : 1.118 ------------------------------------------------------------------------------- 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 111 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 H 82 HIS L 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.095309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057204 restraints weight = 55473.169| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.27 r_work: 0.2880 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15393 Z= 0.174 Angle : 0.568 6.751 22030 Z= 0.331 Chirality : 0.035 0.143 2494 Planarity : 0.004 0.045 1779 Dihedral : 29.893 174.665 4400 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.44 % Allowed : 9.75 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1054 helix: 1.62 (0.20), residues: 718 sheet: 0.94 (0.71), residues: 42 loop : -0.35 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 325 HIS 0.006 0.001 HIS L 135 PHE 0.008 0.001 PHE L 181 TYR 0.023 0.001 TYR L 322 ARG 0.006 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 900) hydrogen bonds : angle 3.33315 ( 2295) covalent geometry : bond 0.00390 (15393) covalent geometry : angle 0.56833 (22030) *********************** 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 152 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9215 (mtm) cc_final: 0.8806 (mtm) REVERT: B 25 ASN cc_start: 0.8463 (m110) cc_final: 0.7966 (m110) REVERT: B 78 ARG cc_start: 0.8925 (ptt90) cc_final: 0.8566 (ptt90) REVERT: D 33 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8162 (tpt-90) REVERT: E 59 GLU cc_start: 0.7865 (pm20) cc_final: 0.6957 (pm20) REVERT: E 81 ASP cc_start: 0.8793 (t70) cc_final: 0.8318 (t70) REVERT: E 97 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8255 (tt0) REVERT: E 125 GLN cc_start: 0.8906 (mp10) cc_final: 0.8108 (mp10) REVERT: G 72 ASP cc_start: 0.9267 (m-30) cc_final: 0.9020 (m-30) REVERT: G 90 ASP cc_start: 0.8494 (t70) cc_final: 0.8233 (t0) REVERT: G 104 GLN cc_start: 0.8551 (pm20) cc_final: 0.8347 (pm20) REVERT: H 68 ASP cc_start: 0.8981 (t0) cc_final: 0.8593 (t0) REVERT: H 71 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8963 (tm-30) REVERT: H 84 ASN cc_start: 0.9008 (t0) cc_final: 0.8704 (t0) REVERT: L 158 MET cc_start: 0.5331 (ptp) cc_final: 0.5091 (ptt) outliers start: 13 outliers final: 7 residues processed: 147 average time/residue: 0.3040 time to fit residues: 63.2931 Evaluate side-chains 133 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 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 40 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.095064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056521 restraints weight = 56129.110| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.27 r_work: 0.2868 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15393 Z= 0.173 Angle : 0.547 5.499 22030 Z= 0.321 Chirality : 0.035 0.143 2494 Planarity : 0.004 0.044 1779 Dihedral : 29.867 175.087 4392 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 11.85 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1054 helix: 1.93 (0.20), residues: 712 sheet: 1.18 (0.62), residues: 41 loop : -0.27 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 325 HIS 0.005 0.001 HIS L 135 PHE 0.010 0.001 PHE A 67 TYR 0.026 0.002 TYR B 88 ARG 0.004 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 900) hydrogen bonds : angle 3.16343 ( 2295) covalent geometry : bond 0.00392 (15393) covalent geometry : angle 0.54695 (22030) *********************** 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 157 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8718 (mm) cc_final: 0.8507 (mt) REVERT: A 94 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8865 (tt0) REVERT: A 120 MET cc_start: 0.9202 (mtm) cc_final: 0.8844 (mtm) REVERT: B 25 ASN cc_start: 0.8525 (m110) cc_final: 0.8037 (m110) REVERT: E 59 GLU cc_start: 0.7913 (pm20) cc_final: 0.7326 (pm20) REVERT: E 81 ASP cc_start: 0.8778 (t70) cc_final: 0.8309 (t70) REVERT: E 97 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8364 (tt0) REVERT: E 107 THR cc_start: 0.9422 (m) cc_final: 0.9135 (t) REVERT: G 90 ASP cc_start: 0.8502 (t70) cc_final: 0.8170 (t0) REVERT: H 68 ASP cc_start: 0.8991 (t0) cc_final: 0.8645 (t0) REVERT: H 71 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8955 (tm-30) REVERT: H 76 GLU cc_start: 0.8995 (tp30) cc_final: 0.8700 (tp30) REVERT: H 84 ASN cc_start: 0.8998 (t0) cc_final: 0.8669 (t0) REVERT: L 155 MET cc_start: -0.5117 (ttt) cc_final: -0.5745 (ttt) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.3042 time to fit residues: 65.5001 Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 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 F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR 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 129 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 121 optimal weight: 50.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.094913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056675 restraints weight = 55771.682| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.34 r_work: 0.2837 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15393 Z= 0.180 Angle : 0.553 6.936 22030 Z= 0.322 Chirality : 0.035 0.142 2494 Planarity : 0.004 0.044 1779 Dihedral : 29.887 174.956 4388 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.10 % Allowed : 13.73 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1054 helix: 1.99 (0.20), residues: 713 sheet: 1.40 (0.62), residues: 41 loop : -0.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 PHE 0.009 0.001 PHE E 67 TYR 0.041 0.002 TYR H 83 ARG 0.003 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 900) hydrogen bonds : angle 3.11683 ( 2295) covalent geometry : bond 0.00411 (15393) covalent geometry : angle 0.55261 (22030) *********************** 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 154 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8854 (m) cc_final: 0.8452 (p) REVERT: A 120 MET cc_start: 0.9169 (mtm) cc_final: 0.8811 (mtm) REVERT: B 25 ASN cc_start: 0.8546 (m110) cc_final: 0.8010 (m110) REVERT: B 78 ARG cc_start: 0.9025 (ptt90) cc_final: 0.8795 (ptt90) REVERT: E 59 GLU cc_start: 0.7806 (pm20) cc_final: 0.7123 (pm20) REVERT: E 81 ASP cc_start: 0.8784 (t70) cc_final: 0.8308 (t70) REVERT: E 97 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8341 (tt0) REVERT: E 107 THR cc_start: 0.9403 (m) cc_final: 0.9129 (t) REVERT: H 68 ASP cc_start: 0.9002 (t0) cc_final: 0.8627 (t0) REVERT: H 71 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8940 (tm-30) REVERT: H 76 GLU cc_start: 0.8944 (tp30) cc_final: 0.8731 (tp30) REVERT: H 84 ASN cc_start: 0.9024 (t0) cc_final: 0.8718 (t0) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 0.2902 time to fit residues: 60.4885 Evaluate side-chains 140 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 93 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3982 r_free = 0.3982 target = 0.095316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057010 restraints weight = 56639.190| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.35 r_work: 0.2854 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15393 Z= 0.155 Angle : 0.542 6.152 22030 Z= 0.317 Chirality : 0.034 0.142 2494 Planarity : 0.004 0.043 1779 Dihedral : 29.875 174.398 4388 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.88 % Allowed : 14.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.26), residues: 1054 helix: 2.09 (0.20), residues: 713 sheet: 1.48 (0.62), residues: 41 loop : -0.32 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 PHE 0.008 0.001 PHE E 67 TYR 0.018 0.002 TYR H 83 ARG 0.004 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 900) hydrogen bonds : angle 3.02995 ( 2295) covalent geometry : bond 0.00348 (15393) covalent geometry : angle 0.54207 (22030) *********************** 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 154 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8862 (m) cc_final: 0.8475 (p) REVERT: A 120 MET cc_start: 0.9162 (mtm) cc_final: 0.8800 (mtm) REVERT: B 25 ASN cc_start: 0.8506 (m110) cc_final: 0.7965 (m110) REVERT: B 78 ARG cc_start: 0.9039 (ptt90) cc_final: 0.8798 (ptt90) REVERT: C 90 ASP cc_start: 0.7585 (t0) cc_final: 0.7156 (t0) REVERT: E 81 ASP cc_start: 0.8807 (t70) cc_final: 0.8322 (t70) REVERT: E 97 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8362 (tt0) REVERT: E 107 THR cc_start: 0.9405 (m) cc_final: 0.9120 (t) REVERT: G 95 LYS cc_start: 0.9323 (tmmt) cc_final: 0.8877 (tmmt) REVERT: H 68 ASP cc_start: 0.9000 (t0) cc_final: 0.8611 (t0) REVERT: H 71 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8932 (tm-30) REVERT: H 84 ASN cc_start: 0.8984 (t0) cc_final: 0.8522 (t0) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.2940 time to fit residues: 61.9907 Evaluate side-chains 141 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 93 GLU 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 100 VAL 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 34 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 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 = 0.3983 r_free = 0.3983 target = 0.095339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057095 restraints weight = 56346.402| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.28 r_work: 0.2879 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15393 Z= 0.158 Angle : 0.541 5.810 22030 Z= 0.316 Chirality : 0.034 0.142 2494 Planarity : 0.004 0.043 1779 Dihedral : 29.875 174.265 4388 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.55 % Allowed : 15.06 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.26), residues: 1054 helix: 2.10 (0.20), residues: 712 sheet: 1.53 (0.62), residues: 41 loop : -0.32 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 PHE 0.007 0.001 PHE E 67 TYR 0.021 0.002 TYR H 83 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 900) hydrogen bonds : angle 3.00986 ( 2295) covalent geometry : bond 0.00355 (15393) covalent geometry : angle 0.54143 (22030) *********************** 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 : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8913 (m) cc_final: 0.8526 (p) REVERT: A 120 MET cc_start: 0.9142 (mtm) cc_final: 0.8790 (mtm) REVERT: B 25 ASN cc_start: 0.8608 (m-40) cc_final: 0.7964 (m-40) REVERT: B 78 ARG cc_start: 0.9057 (ptt90) cc_final: 0.8810 (ptt90) REVERT: E 81 ASP cc_start: 0.8799 (t70) cc_final: 0.8341 (t70) REVERT: E 97 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8400 (tt0) REVERT: E 107 THR cc_start: 0.9415 (m) cc_final: 0.9129 (t) REVERT: H 68 ASP cc_start: 0.9009 (t0) cc_final: 0.8638 (t0) REVERT: H 71 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8934 (tm-30) REVERT: H 84 ASN cc_start: 0.8983 (t0) cc_final: 0.8461 (t0) REVERT: H 86 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7768 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 0.2858 time to fit residues: 61.3301 Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER 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 62 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 131 optimal weight: 50.0000 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3995 r_free = 0.3995 target = 0.096041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058230 restraints weight = 56529.938| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.32 r_work: 0.2880 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15393 Z= 0.139 Angle : 0.535 6.649 22030 Z= 0.313 Chirality : 0.033 0.142 2494 Planarity : 0.004 0.043 1779 Dihedral : 29.851 173.721 4388 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.66 % Allowed : 16.06 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1054 helix: 2.12 (0.20), residues: 712 sheet: 1.99 (0.69), residues: 29 loop : -0.19 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 325 HIS 0.004 0.001 HIS L 135 PHE 0.008 0.001 PHE A 67 TYR 0.026 0.002 TYR H 83 ARG 0.005 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 900) hydrogen bonds : angle 2.96620 ( 2295) covalent geometry : bond 0.00306 (15393) covalent geometry : angle 0.53543 (22030) *********************** 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: 15 poor density : 137 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8853 (m) cc_final: 0.8482 (p) REVERT: A 120 MET cc_start: 0.9128 (mtm) cc_final: 0.8768 (mtm) REVERT: B 25 ASN cc_start: 0.8550 (m-40) cc_final: 0.8067 (m-40) REVERT: B 78 ARG cc_start: 0.9067 (ptt90) cc_final: 0.8796 (ptt90) REVERT: E 81 ASP cc_start: 0.8823 (t70) cc_final: 0.8168 (t70) REVERT: E 97 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8382 (tt0) REVERT: E 107 THR cc_start: 0.9395 (m) cc_final: 0.9103 (t) REVERT: H 68 ASP cc_start: 0.8987 (t0) cc_final: 0.8608 (t0) REVERT: H 71 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8920 (tm-30) REVERT: H 84 ASN cc_start: 0.8875 (t0) cc_final: 0.8443 (t0) REVERT: L 236 MET cc_start: 0.7359 (ptt) cc_final: 0.6961 (mpp) outliers start: 15 outliers final: 13 residues processed: 146 average time/residue: 0.3214 time to fit residues: 66.9186 Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL 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 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 46 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 40.0000 chunk 5 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3995 r_free = 0.3995 target = 0.096103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.058070 restraints weight = 55532.051| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.35 r_work: 0.2884 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15393 Z= 0.141 Angle : 0.532 7.718 22030 Z= 0.311 Chirality : 0.033 0.142 2494 Planarity : 0.004 0.043 1779 Dihedral : 29.836 173.673 4388 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 16.72 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.26), residues: 1054 helix: 2.08 (0.20), residues: 712 sheet: 1.87 (0.71), residues: 29 loop : -0.19 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 325 HIS 0.004 0.001 HIS G 31 PHE 0.007 0.001 PHE A 67 TYR 0.028 0.002 TYR H 83 ARG 0.010 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 900) hydrogen bonds : angle 2.97531 ( 2295) covalent geometry : bond 0.00309 (15393) covalent geometry : angle 0.53214 (22030) *********************** 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 146 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8869 (m) cc_final: 0.8500 (p) REVERT: A 120 MET cc_start: 0.9112 (mtm) cc_final: 0.8777 (mtm) REVERT: B 25 ASN cc_start: 0.8678 (m-40) cc_final: 0.7812 (m110) REVERT: B 78 ARG cc_start: 0.9072 (ptt90) cc_final: 0.8789 (ptt90) REVERT: E 81 ASP cc_start: 0.8728 (t70) cc_final: 0.8199 (t70) REVERT: E 97 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8398 (tt0) REVERT: E 107 THR cc_start: 0.9382 (m) cc_final: 0.9089 (t) REVERT: E 126 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (tt) REVERT: G 42 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8634 (mtm110) REVERT: H 68 ASP cc_start: 0.8999 (t0) cc_final: 0.8751 (t0) REVERT: H 84 ASN cc_start: 0.8825 (t0) cc_final: 0.8438 (t0) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.2886 time to fit residues: 57.4640 Evaluate side-chains 139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 37 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL 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 126 LEU Chi-restraints excluded: chain F residue 62 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 120 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 129 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3969 r_free = 0.3969 target = 0.095001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056097 restraints weight = 56357.226| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.28 r_work: 0.2835 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15393 Z= 0.221 Angle : 0.589 8.741 22030 Z= 0.341 Chirality : 0.036 0.144 2494 Planarity : 0.004 0.044 1779 Dihedral : 30.036 175.428 4388 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.33 % Allowed : 16.39 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1054 helix: 1.94 (0.20), residues: 712 sheet: 1.39 (0.63), residues: 41 loop : -0.31 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 325 HIS 0.009 0.001 HIS G 31 PHE 0.010 0.001 PHE A 104 TYR 0.032 0.002 TYR H 83 ARG 0.018 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 900) hydrogen bonds : angle 3.19182 ( 2295) covalent geometry : bond 0.00511 (15393) covalent geometry : angle 0.58948 (22030) *********************** 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 145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8808 (m) cc_final: 0.8364 (p) REVERT: A 120 MET cc_start: 0.9142 (mtm) cc_final: 0.8936 (mtm) REVERT: B 25 ASN cc_start: 0.8807 (m-40) cc_final: 0.7996 (m110) REVERT: B 78 ARG cc_start: 0.9030 (ptt90) cc_final: 0.8713 (ptt90) REVERT: C 90 ASP cc_start: 0.7923 (t0) cc_final: 0.7350 (t0) REVERT: E 81 ASP cc_start: 0.8686 (t70) cc_final: 0.8194 (t70) REVERT: E 97 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8418 (tt0) REVERT: E 107 THR cc_start: 0.9387 (m) cc_final: 0.9093 (t) REVERT: E 126 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8508 (tt) REVERT: G 95 LYS cc_start: 0.9284 (tttm) cc_final: 0.8934 (tmmt) REVERT: H 68 ASP cc_start: 0.9082 (t0) cc_final: 0.8751 (t0) REVERT: H 84 ASN cc_start: 0.9001 (t0) cc_final: 0.8614 (t0) REVERT: L 236 MET cc_start: 0.7295 (ptt) cc_final: 0.6871 (mpp) outliers start: 21 outliers final: 15 residues processed: 138 average time/residue: 0.2697 time to fit residues: 54.0889 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 : 2.270 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 62 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 122 optimal weight: 50.0000 chunk 108 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 107 optimal weight: 0.0170 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** 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 = 0.3999 r_free = 0.3999 target = 0.096620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058399 restraints weight = 56894.332| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.54 r_work: 0.2895 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15393 Z= 0.146 Angle : 0.555 7.189 22030 Z= 0.322 Chirality : 0.034 0.186 2494 Planarity : 0.004 0.044 1779 Dihedral : 29.902 173.318 4388 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.55 % Allowed : 17.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1054 helix: 2.01 (0.20), residues: 710 sheet: 1.44 (0.62), residues: 41 loop : -0.26 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 325 HIS 0.004 0.001 HIS L 34 PHE 0.008 0.001 PHE E 67 TYR 0.042 0.002 TYR H 83 ARG 0.010 0.000 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 900) hydrogen bonds : angle 3.07338 ( 2295) covalent geometry : bond 0.00326 (15393) covalent geometry : angle 0.55466 (22030) ********************** 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 144 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.8828 (m) cc_final: 0.8355 (p) REVERT: A 120 MET cc_start: 0.9126 (mtm) cc_final: 0.8773 (mtm) REVERT: B 78 ARG cc_start: 0.9056 (ptt90) cc_final: 0.8767 (ptt90) REVERT: C 90 ASP cc_start: 0.7786 (t0) cc_final: 0.7194 (t0) REVERT: E 81 ASP cc_start: 0.8690 (t70) cc_final: 0.8209 (t70) REVERT: E 97 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8381 (tt0) REVERT: E 107 THR cc_start: 0.9381 (m) cc_final: 0.9078 (t) REVERT: E 120 MET cc_start: 0.8993 (mtm) cc_final: 0.8579 (mtm) REVERT: E 126 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8450 (tt) REVERT: G 95 LYS cc_start: 0.9194 (tttm) cc_final: 0.8854 (tmmt) REVERT: H 68 ASP cc_start: 0.9059 (t0) cc_final: 0.8783 (t0) REVERT: H 84 ASN cc_start: 0.8877 (t0) cc_final: 0.8564 (t0) REVERT: L 236 MET cc_start: 0.7289 (ptt) cc_final: 0.6896 (mpp) outliers start: 14 outliers final: 13 residues processed: 140 average time/residue: 0.3340 time to fit residues: 69.5155 Evaluate side-chains 137 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 126 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.0870 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4024 r_free = 0.4024 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060343 restraints weight = 57352.294| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.42 r_work: 0.2950 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15393 Z= 0.134 Angle : 0.546 8.870 22030 Z= 0.316 Chirality : 0.033 0.170 2494 Planarity : 0.004 0.045 1779 Dihedral : 29.796 173.116 4388 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.44 % Allowed : 18.49 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.26), residues: 1054 helix: 2.05 (0.20), residues: 710 sheet: 1.89 (0.68), residues: 29 loop : -0.04 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 325 HIS 0.006 0.001 HIS F 75 PHE 0.006 0.001 PHE B 100 TYR 0.038 0.001 TYR D 40 ARG 0.010 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 900) hydrogen bonds : angle 2.98618 ( 2295) covalent geometry : bond 0.00291 (15393) covalent geometry : angle 0.54561 (22030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10841.08 seconds wall clock time: 187 minutes 11.56 seconds (11231.56 seconds total)