Starting phenix.real_space_refine on Thu Mar 13 18:40:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.map" model { file = "/net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cii_16676/03_2025/8cii_16676.cif" } resolution = 2.7 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5696 2.51 5 N 1513 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9024 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "H" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1657 Classifications: {'peptide': 217} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1622 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 200} Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1644 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 207} Chain breaks: 1 Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain: "C" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.80, per 1000 atoms: 0.75 Number of scatterers: 9024 At special positions: 0 Unit cell: (78.8724, 127.802, 140.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1784 8.00 N 1513 7.00 C 5696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN E 343 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 26 sheets defined 11.3% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.958A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.958A pdb=" N TYR H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.021A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 194 through 198 removed outlier: 3.520A pdb=" N SER H 197 " --> pdb=" O PRO H 194 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU H 198 " --> pdb=" O SER H 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 194 through 198' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.746A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.578A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.528A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.510A pdb=" N LEU A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 3.501A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.251A pdb=" N HIS H 33 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.898A pdb=" N CYS H 95 " --> pdb=" O TRP H 112 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP H 112 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG H 97 " --> pdb=" O ASP H 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.649A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.649A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.273A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.875A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.353A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.620A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB5, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.448A pdb=" N ILE A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.564A pdb=" N SER A 193 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.564A pdb=" N SER A 193 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 164 through 167 removed outlier: 4.402A pdb=" N TYR A 207 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.640A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.523A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.797A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.667A pdb=" N TYR C 113 " --> pdb=" O ALA C 98 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2868 1.34 - 1.46: 2166 1.46 - 1.58: 4176 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 9247 Sorted by residual: bond pdb=" C2 FUC D 4 " pdb=" C3 FUC D 4 " ideal model delta sigma weight residual 1.526 1.499 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C3 FUC D 4 " pdb=" C4 FUC D 4 " ideal model delta sigma weight residual 1.529 1.502 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.54e+00 bond pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.41e+00 bond pdb=" C GLN B 38 " pdb=" N LYS B 39 " ideal model delta sigma weight residual 1.339 1.273 0.066 5.57e-02 3.22e+02 1.41e+00 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12150 1.27 - 2.53: 337 2.53 - 3.80: 82 3.80 - 5.06: 12 5.06 - 6.33: 6 Bond angle restraints: 12587 Sorted by residual: angle pdb=" N LEU A 137 " pdb=" CA LEU A 137 " pdb=" C LEU A 137 " ideal model delta sigma weight residual 109.62 105.42 4.20 1.50e+00 4.44e-01 7.82e+00 angle pdb=" C PHE A 29 " pdb=" N SER A 30 " pdb=" CA SER A 30 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.23e+00 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 113.20 109.64 3.56 1.36e+00 5.41e-01 6.85e+00 angle pdb=" N LEU H 133 " pdb=" CA LEU H 133 " pdb=" C LEU H 133 " ideal model delta sigma weight residual 109.62 105.70 3.92 1.50e+00 4.44e-01 6.84e+00 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.58 114.07 -3.49 1.35e+00 5.49e-01 6.69e+00 ... (remaining 12582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 5364 21.17 - 42.34: 135 42.34 - 63.50: 22 63.50 - 84.67: 10 84.67 - 105.84: 5 Dihedral angle restraints: 5536 sinusoidal: 2161 harmonic: 3375 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.13 105.84 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.29 104.91 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" N PRO A 53 " pdb=" CA PRO A 53 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1130 0.050 - 0.100: 214 0.100 - 0.150: 66 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.17e+00 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.15e+00 ... (remaining 1408 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 157 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO H 158 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 158 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 158 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 161 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 162 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 155 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO H 156 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.020 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1967 2.78 - 3.31: 7769 3.31 - 3.84: 14911 3.84 - 4.37: 17688 4.37 - 4.90: 31191 Nonbonded interactions: 73526 Sorted by model distance: nonbonded pdb=" O GLN B 124 " pdb=" OG SER B 127 " model vdw 2.253 3.040 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.268 3.040 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 30 " pdb=" N SER B 31 " model vdw 2.298 3.120 nonbonded pdb=" O LEU A 111 " pdb=" ND2 ASN B 34 " model vdw 2.317 3.120 ... (remaining 73521 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 'B' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 29 or \ resid 33 or resid 35 through 45 or resid 47 through 49 or resid 52 through 54 o \ r resid 56 through 69 or resid 71 through 76 or resid 78 through 80 or resid 82 \ through 90 or resid 93 or resid 98 through 211)) selection = (chain 'L' and (resid 1 through 2 or resid 5 through 9 or resid 11 through 29 or \ resid 33 or resid 35 through 45 or resid 47 through 49 or resid 52 through 54 o \ r resid 56 through 69 or resid 71 through 76 or resid 78 through 80 or resid 82 \ through 90 or resid 93 or resid 98 through 211)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.680 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.850 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 0.066 9247 Z= 0.344 Angle : 0.566 6.326 12587 Z= 0.306 Chirality : 0.043 0.250 1411 Planarity : 0.004 0.043 1605 Dihedral : 10.814 105.840 3344 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.40 % Allowed : 3.36 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.69 (0.26), residues: 1152 helix: -1.61 (0.61), residues: 55 sheet: 1.04 (0.25), residues: 497 loop : 0.25 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 116 HIS 0.003 0.001 HIS A 108 PHE 0.012 0.001 PHE E 456 TYR 0.016 0.001 TYR H 50 ARG 0.003 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 1.028 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8325 (tp30) REVERT: E 356 LYS cc_start: 0.8809 (tttp) cc_final: 0.8592 (tttt) REVERT: E 390 LEU cc_start: 0.8855 (mt) cc_final: 0.8553 (mt) REVERT: E 392 PHE cc_start: 0.7804 (m-80) cc_final: 0.7599 (m-80) REVERT: E 462 LYS cc_start: 0.8431 (mttp) cc_final: 0.8172 (mtpm) REVERT: H 3 GLN cc_start: 0.9127 (mt0) cc_final: 0.8734 (mp10) REVERT: H 16 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8121 (mm-30) REVERT: H 75 LYS cc_start: 0.9619 (mttp) cc_final: 0.9136 (mtmm) REVERT: H 129 SER cc_start: 0.8912 (m) cc_final: 0.8634 (p) REVERT: H 185 TYR cc_start: 0.8764 (m-80) cc_final: 0.8364 (m-10) REVERT: L 81 ASP cc_start: 0.9057 (m-30) cc_final: 0.8683 (t0) REVERT: L 90 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8955 (pp30) REVERT: L 106 ILE cc_start: 0.9027 (mt) cc_final: 0.8761 (mt) REVERT: L 134 CYS cc_start: 0.7835 (t) cc_final: 0.7490 (t) REVERT: L 167 ASP cc_start: 0.7287 (t70) cc_final: 0.6789 (t0) REVERT: L 170 ASP cc_start: 0.8873 (p0) cc_final: 0.8605 (p0) REVERT: A 10 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7483 (mp0) REVERT: A 12 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8826 (mptp) REVERT: A 23 LYS cc_start: 0.9337 (tttm) cc_final: 0.9093 (tttm) REVERT: A 43 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7578 (mp10) REVERT: A 65 GLN cc_start: 0.8930 (tp40) cc_final: 0.8646 (pm20) REVERT: A 82 GLU cc_start: 0.9050 (tt0) cc_final: 0.8485 (tm-30) REVERT: A 130 LYS cc_start: 0.8541 (tttm) cc_final: 0.7915 (mmtp) REVERT: A 156 LYS cc_start: 0.8794 (tttp) cc_final: 0.8469 (mtpp) REVERT: A 157 ASP cc_start: 0.8617 (m-30) cc_final: 0.8302 (m-30) REVERT: A 219 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8931 (mptt) REVERT: B 82 ASP cc_start: 0.8222 (m-30) cc_final: 0.7790 (m-30) REVERT: B 106 ILE cc_start: 0.9291 (mt) cc_final: 0.9091 (mt) REVERT: B 140 TYR cc_start: 0.9133 (t80) cc_final: 0.8632 (t80) REVERT: B 164 THR cc_start: 0.8991 (p) cc_final: 0.8785 (t) REVERT: C 65 LYS cc_start: 0.9076 (tttt) cc_final: 0.8826 (tppp) REVERT: C 76 ASN cc_start: 0.9224 (p0) cc_final: 0.8716 (p0) REVERT: C 77 ASN cc_start: 0.9152 (t0) cc_final: 0.8906 (p0) REVERT: C 83 MET cc_start: 0.9249 (mtm) cc_final: 0.8990 (mmm) REVERT: C 93 ILE cc_start: 0.9330 (mt) cc_final: 0.9055 (mm) outliers start: 4 outliers final: 2 residues processed: 236 average time/residue: 1.4206 time to fit residues: 354.5116 Evaluate side-chains 167 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.0670 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 474 GLN L 147 GLN A 59 ASN A 205 GLN B 6 GLN B 92 HIS B 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054801 restraints weight = 20951.693| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.69 r_work: 0.2681 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9247 Z= 0.261 Angle : 0.632 9.486 12587 Z= 0.327 Chirality : 0.045 0.141 1411 Planarity : 0.005 0.049 1605 Dihedral : 6.919 66.628 1346 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.29 % Allowed : 12.46 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.85 (0.26), residues: 1152 helix: -1.90 (0.61), residues: 58 sheet: 1.22 (0.24), residues: 504 loop : 0.34 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 167 HIS 0.004 0.001 HIS L 198 PHE 0.016 0.001 PHE A 135 TYR 0.021 0.001 TYR L 173 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.045 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8359 (tp30) REVERT: E 386 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9120 (mmtp) REVERT: E 390 LEU cc_start: 0.8936 (mt) cc_final: 0.8651 (mp) REVERT: E 462 LYS cc_start: 0.8257 (mttp) cc_final: 0.8008 (mtpm) REVERT: H 3 GLN cc_start: 0.8986 (mt0) cc_final: 0.8589 (mp10) REVERT: H 16 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8063 (mm-30) REVERT: H 72 ASP cc_start: 0.7122 (t0) cc_final: 0.6245 (t0) REVERT: H 75 LYS cc_start: 0.9499 (mttp) cc_final: 0.9287 (mtmm) REVERT: H 129 SER cc_start: 0.8005 (m) cc_final: 0.7714 (p) REVERT: L 17 ASP cc_start: 0.8841 (t0) cc_final: 0.7916 (m-30) REVERT: L 70 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7542 (mp0) REVERT: L 81 ASP cc_start: 0.9289 (m-30) cc_final: 0.8688 (t0) REVERT: L 90 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8580 (pp30) REVERT: A 12 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8670 (mptp) REVERT: A 23 LYS cc_start: 0.9184 (tttm) cc_final: 0.8931 (tttm) REVERT: A 80 TYR cc_start: 0.8796 (m-80) cc_final: 0.8523 (m-10) REVERT: A 82 GLU cc_start: 0.9210 (tt0) cc_final: 0.8482 (tm-30) REVERT: A 130 LYS cc_start: 0.8073 (tttm) cc_final: 0.7785 (tptm) REVERT: A 167 TRP cc_start: 0.8128 (m100) cc_final: 0.7879 (m100) REVERT: A 207 TYR cc_start: 0.8604 (m-80) cc_final: 0.8039 (m-80) REVERT: A 219 LYS cc_start: 0.9213 (mtpt) cc_final: 0.8824 (mmtt) REVERT: B 24 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7678 (ttm110) REVERT: B 82 ASP cc_start: 0.8290 (m-30) cc_final: 0.7435 (m-30) REVERT: B 143 GLU cc_start: 0.7638 (pm20) cc_final: 0.5344 (pm20) REVERT: C 39 GLN cc_start: 0.9274 (tt0) cc_final: 0.8784 (tp40) REVERT: C 43 LYS cc_start: 0.9348 (mmmm) cc_final: 0.8931 (mptt) REVERT: C 65 LYS cc_start: 0.9086 (tttt) cc_final: 0.8790 (tppp) REVERT: C 76 ASN cc_start: 0.9309 (p0) cc_final: 0.8770 (p0) REVERT: C 77 ASN cc_start: 0.9157 (t0) cc_final: 0.8869 (p0) REVERT: C 80 TYR cc_start: 0.8700 (m-80) cc_final: 0.8203 (m-80) REVERT: C 83 MET cc_start: 0.9290 (mtm) cc_final: 0.9012 (mtm) REVERT: C 85 MET cc_start: 0.9206 (mpp) cc_final: 0.8904 (mpp) REVERT: C 93 ILE cc_start: 0.8817 (mt) cc_final: 0.8568 (mm) REVERT: C 105 ASP cc_start: 0.8723 (t0) cc_final: 0.8490 (t0) outliers start: 13 outliers final: 5 residues processed: 187 average time/residue: 1.5633 time to fit residues: 310.4914 Evaluate side-chains 163 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.095841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055396 restraints weight = 21247.157| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.76 r_work: 0.2698 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9247 Z= 0.208 Angle : 0.598 9.486 12587 Z= 0.303 Chirality : 0.045 0.156 1411 Planarity : 0.005 0.048 1605 Dihedral : 5.680 52.428 1344 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 13.25 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.80 (0.25), residues: 1152 helix: -2.22 (0.58), residues: 58 sheet: 1.11 (0.23), residues: 521 loop : 0.40 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.005 0.001 HIS L 189 PHE 0.025 0.001 PHE H 131 TYR 0.042 0.001 TYR L 140 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.051 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: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8389 (tp30) REVERT: E 462 LYS cc_start: 0.8244 (mttp) cc_final: 0.7980 (mtpm) REVERT: H 3 GLN cc_start: 0.8888 (mt0) cc_final: 0.8493 (mp10) REVERT: H 16 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8051 (mm-30) REVERT: H 43 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8622 (mmmm) REVERT: H 46 GLU cc_start: 0.8874 (tt0) cc_final: 0.8589 (tt0) REVERT: H 72 ASP cc_start: 0.7237 (t0) cc_final: 0.6167 (t0) REVERT: H 75 LYS cc_start: 0.9509 (mttp) cc_final: 0.9262 (mtmm) REVERT: H 219 ARG cc_start: 0.9122 (ttt180) cc_final: 0.8823 (tpt170) REVERT: L 17 ASP cc_start: 0.8880 (t0) cc_final: 0.7871 (m-30) REVERT: L 70 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7542 (mp0) REVERT: L 81 ASP cc_start: 0.9296 (m-30) cc_final: 0.8708 (t0) REVERT: L 90 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8566 (pp30) REVERT: L 142 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8666 (mmm-85) REVERT: A 23 LYS cc_start: 0.9170 (tttm) cc_final: 0.8911 (tttm) REVERT: A 80 TYR cc_start: 0.8791 (m-80) cc_final: 0.8554 (m-10) REVERT: A 82 GLU cc_start: 0.9166 (tt0) cc_final: 0.8436 (tm-30) REVERT: A 89 ASP cc_start: 0.9090 (m-30) cc_final: 0.8423 (p0) REVERT: A 98 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7964 (ttp-110) REVERT: A 130 LYS cc_start: 0.8126 (tttm) cc_final: 0.7856 (tptm) REVERT: A 207 TYR cc_start: 0.8710 (m-80) cc_final: 0.7931 (m-80) REVERT: A 219 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8871 (mmtt) REVERT: A 222 LYS cc_start: 0.7866 (tptp) cc_final: 0.7560 (tptp) REVERT: B 24 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7630 (ttm110) REVERT: B 82 ASP cc_start: 0.8280 (m-30) cc_final: 0.7536 (m-30) REVERT: C 65 LYS cc_start: 0.9131 (tttt) cc_final: 0.8823 (tppp) REVERT: C 76 ASN cc_start: 0.9303 (p0) cc_final: 0.9036 (p0) REVERT: C 77 ASN cc_start: 0.9162 (t0) cc_final: 0.8831 (t0) REVERT: C 80 TYR cc_start: 0.8729 (m-80) cc_final: 0.8149 (m-80) REVERT: C 83 MET cc_start: 0.9305 (mtm) cc_final: 0.9026 (mtm) REVERT: C 93 ILE cc_start: 0.8761 (mt) cc_final: 0.8509 (mm) outliers start: 26 outliers final: 11 residues processed: 181 average time/residue: 1.4024 time to fit residues: 268.9490 Evaluate side-chains 164 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054607 restraints weight = 21118.571| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.73 r_work: 0.2693 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9247 Z= 0.293 Angle : 0.610 9.041 12587 Z= 0.311 Chirality : 0.045 0.166 1411 Planarity : 0.005 0.055 1605 Dihedral : 5.128 53.698 1344 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.77 % Allowed : 13.95 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.76 (0.25), residues: 1152 helix: -2.44 (0.54), residues: 60 sheet: 1.04 (0.22), residues: 528 loop : 0.44 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 167 HIS 0.005 0.001 HIS B 198 PHE 0.017 0.001 PHE B 116 TYR 0.041 0.002 TYR B 140 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.683 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: symmetry clash REVERT: E 340 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8396 (tp30) REVERT: E 386 LYS cc_start: 0.9293 (mmmm) cc_final: 0.8851 (mtmp) REVERT: E 462 LYS cc_start: 0.8221 (mttp) cc_final: 0.7963 (mtpm) REVERT: H 3 GLN cc_start: 0.8880 (mt0) cc_final: 0.8488 (mp10) REVERT: H 27 ASP cc_start: 0.9043 (OUTLIER) cc_final: 0.8813 (m-30) REVERT: H 43 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8564 (mmmm) REVERT: H 72 ASP cc_start: 0.7384 (t0) cc_final: 0.6268 (t0) REVERT: H 75 LYS cc_start: 0.9491 (mttp) cc_final: 0.9204 (mtmm) REVERT: H 219 ARG cc_start: 0.9142 (ttt180) cc_final: 0.8880 (tpt170) REVERT: L 17 ASP cc_start: 0.8881 (t0) cc_final: 0.7875 (m-30) REVERT: L 70 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7599 (mp0) REVERT: L 81 ASP cc_start: 0.9282 (m-30) cc_final: 0.8666 (t0) REVERT: L 90 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8539 (pp30) REVERT: L 142 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8538 (mmm-85) REVERT: A 23 LYS cc_start: 0.9144 (tttm) cc_final: 0.8901 (tttm) REVERT: A 62 GLN cc_start: 0.9337 (mm-40) cc_final: 0.8848 (tp40) REVERT: A 63 LYS cc_start: 0.9295 (ttpp) cc_final: 0.8490 (ttpp) REVERT: A 82 GLU cc_start: 0.9149 (tt0) cc_final: 0.8436 (tm-30) REVERT: A 89 ASP cc_start: 0.9148 (m-30) cc_final: 0.8511 (p0) REVERT: A 98 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: A 207 TYR cc_start: 0.8481 (m-80) cc_final: 0.7955 (m-80) REVERT: A 219 LYS cc_start: 0.9288 (mtpt) cc_final: 0.8880 (mmtt) REVERT: B 82 ASP cc_start: 0.8313 (m-30) cc_final: 0.7577 (m-30) REVERT: B 105 GLU cc_start: 0.7980 (pp20) cc_final: 0.7665 (pp20) REVERT: C 39 GLN cc_start: 0.9066 (tt0) cc_final: 0.8774 (tp40) REVERT: C 45 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8294 (mtp85) REVERT: C 65 LYS cc_start: 0.9152 (tttt) cc_final: 0.8858 (tppp) REVERT: C 76 ASN cc_start: 0.9278 (p0) cc_final: 0.9027 (p0) REVERT: C 77 ASN cc_start: 0.9173 (t0) cc_final: 0.8855 (t0) REVERT: C 80 TYR cc_start: 0.8807 (m-80) cc_final: 0.8234 (m-80) REVERT: C 85 MET cc_start: 0.9217 (mpp) cc_final: 0.8956 (mpp) REVERT: C 93 ILE cc_start: 0.8833 (mt) cc_final: 0.8555 (mm) REVERT: C 105 ASP cc_start: 0.9029 (t0) cc_final: 0.8803 (t0) outliers start: 28 outliers final: 12 residues processed: 168 average time/residue: 1.6798 time to fit residues: 300.5068 Evaluate side-chains 162 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.054959 restraints weight = 21042.113| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.73 r_work: 0.2703 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9247 Z= 0.229 Angle : 0.605 9.449 12587 Z= 0.306 Chirality : 0.045 0.191 1411 Planarity : 0.004 0.044 1605 Dihedral : 4.941 53.586 1344 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 15.23 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.81 (0.25), residues: 1152 helix: -2.25 (0.57), residues: 60 sheet: 1.10 (0.22), residues: 527 loop : 0.44 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 167 HIS 0.002 0.001 HIS A 213 PHE 0.008 0.001 PHE H 78 TYR 0.029 0.001 TYR B 140 ARG 0.009 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8377 (tp30) REVERT: E 357 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8273 (ttm-80) REVERT: E 462 LYS cc_start: 0.8214 (mttp) cc_final: 0.7945 (mtpp) REVERT: H 3 GLN cc_start: 0.8851 (mt0) cc_final: 0.8467 (mp10) REVERT: H 43 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8577 (mmmm) REVERT: H 72 ASP cc_start: 0.7409 (t0) cc_final: 0.6232 (t0) REVERT: H 75 LYS cc_start: 0.9486 (mttp) cc_final: 0.9188 (mtmm) REVERT: H 219 ARG cc_start: 0.9134 (ttt180) cc_final: 0.8845 (tpt170) REVERT: L 17 ASP cc_start: 0.8908 (t0) cc_final: 0.7921 (m-30) REVERT: L 70 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7547 (mp0) REVERT: L 81 ASP cc_start: 0.9279 (m-30) cc_final: 0.8658 (t0) REVERT: L 90 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8552 (pp30) REVERT: L 142 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8526 (mmm-85) REVERT: A 23 LYS cc_start: 0.9143 (tttm) cc_final: 0.8910 (tttm) REVERT: A 62 GLN cc_start: 0.9360 (mm-40) cc_final: 0.8796 (tp40) REVERT: A 63 LYS cc_start: 0.9299 (ttpp) cc_final: 0.8525 (ttpp) REVERT: A 73 ASP cc_start: 0.8403 (t0) cc_final: 0.7885 (t0) REVERT: A 82 GLU cc_start: 0.9098 (tt0) cc_final: 0.8403 (tm-30) REVERT: A 89 ASP cc_start: 0.9128 (m-30) cc_final: 0.8509 (p0) REVERT: A 98 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7974 (ttp-110) REVERT: A 207 TYR cc_start: 0.8396 (m-80) cc_final: 0.7978 (m-80) REVERT: A 219 LYS cc_start: 0.9290 (mtpt) cc_final: 0.8896 (mmtt) REVERT: B 82 ASP cc_start: 0.8364 (m-30) cc_final: 0.7562 (m-30) REVERT: C 39 GLN cc_start: 0.8953 (tt0) cc_final: 0.8592 (tp40) REVERT: C 45 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8184 (mtp85) REVERT: C 65 LYS cc_start: 0.9150 (tttt) cc_final: 0.8860 (tppp) REVERT: C 76 ASN cc_start: 0.9283 (p0) cc_final: 0.9043 (p0) REVERT: C 77 ASN cc_start: 0.9181 (t0) cc_final: 0.8866 (t0) REVERT: C 80 TYR cc_start: 0.8829 (m-80) cc_final: 0.8299 (m-80) REVERT: C 85 MET cc_start: 0.9207 (mpp) cc_final: 0.8927 (mpp) REVERT: C 93 ILE cc_start: 0.8771 (mt) cc_final: 0.8470 (mm) REVERT: C 105 ASP cc_start: 0.8980 (t0) cc_final: 0.8761 (t0) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 1.5025 time to fit residues: 269.2461 Evaluate side-chains 155 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN B 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.094058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.053441 restraints weight = 21285.033| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.75 r_work: 0.2665 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9247 Z= 0.374 Angle : 0.652 9.373 12587 Z= 0.331 Chirality : 0.046 0.195 1411 Planarity : 0.005 0.065 1605 Dihedral : 5.025 54.503 1344 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.47 % Allowed : 16.72 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.75 (0.25), residues: 1152 helix: -2.08 (0.61), residues: 53 sheet: 1.04 (0.22), residues: 537 loop : 0.33 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 167 HIS 0.002 0.001 HIS L 189 PHE 0.018 0.001 PHE B 118 TYR 0.028 0.002 TYR B 140 ARG 0.009 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8436 (tp30) REVERT: E 386 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8933 (mmmm) REVERT: E 420 ASP cc_start: 0.8818 (m-30) cc_final: 0.8575 (m-30) REVERT: E 462 LYS cc_start: 0.8219 (mttp) cc_final: 0.7961 (mtpm) REVERT: H 3 GLN cc_start: 0.8874 (mt0) cc_final: 0.8484 (mp10) REVERT: H 27 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8822 (m-30) REVERT: H 43 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8601 (mmmm) REVERT: H 72 ASP cc_start: 0.7562 (t0) cc_final: 0.6350 (t0) REVERT: H 75 LYS cc_start: 0.9465 (mttp) cc_final: 0.9154 (mtmm) REVERT: H 219 ARG cc_start: 0.9152 (ttt180) cc_final: 0.8852 (tpt170) REVERT: L 17 ASP cc_start: 0.8927 (t0) cc_final: 0.7937 (m-30) REVERT: L 70 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7567 (mp0) REVERT: L 81 ASP cc_start: 0.9265 (m-30) cc_final: 0.8648 (t0) REVERT: L 90 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8572 (pp30) REVERT: L 105 GLU cc_start: 0.8244 (pp20) cc_final: 0.7968 (pp20) REVERT: L 142 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8529 (mmm-85) REVERT: A 23 LYS cc_start: 0.9115 (tttm) cc_final: 0.8902 (tttm) REVERT: A 62 GLN cc_start: 0.9397 (mm-40) cc_final: 0.8863 (tp40) REVERT: A 82 GLU cc_start: 0.9088 (tt0) cc_final: 0.8427 (tm-30) REVERT: A 89 ASP cc_start: 0.9166 (m-30) cc_final: 0.8601 (p0) REVERT: A 219 LYS cc_start: 0.9307 (mtpt) cc_final: 0.8907 (mmtt) REVERT: A 223 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7431 (tpt170) REVERT: B 77 ARG cc_start: 0.8954 (tpp-160) cc_final: 0.8675 (tpp-160) REVERT: B 81 GLU cc_start: 0.8763 (pm20) cc_final: 0.8554 (pm20) REVERT: B 82 ASP cc_start: 0.8477 (m-30) cc_final: 0.7649 (m-30) REVERT: B 116 PHE cc_start: 0.8611 (m-10) cc_final: 0.8398 (m-10) REVERT: B 201 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8847 (pp) REVERT: B 210 ASN cc_start: 0.8559 (m-40) cc_final: 0.8298 (p0) REVERT: C 39 GLN cc_start: 0.8936 (tt0) cc_final: 0.8651 (tp40) REVERT: C 45 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: C 65 LYS cc_start: 0.9187 (tttt) cc_final: 0.8911 (tppp) REVERT: C 76 ASN cc_start: 0.9253 (p0) cc_final: 0.9010 (p0) REVERT: C 77 ASN cc_start: 0.9195 (t0) cc_final: 0.8914 (t0) REVERT: C 80 TYR cc_start: 0.8936 (m-80) cc_final: 0.8706 (m-80) REVERT: C 85 MET cc_start: 0.9251 (mpp) cc_final: 0.8953 (mpp) REVERT: C 93 ILE cc_start: 0.8820 (mt) cc_final: 0.8485 (mm) outliers start: 25 outliers final: 9 residues processed: 165 average time/residue: 1.4074 time to fit residues: 246.0744 Evaluate side-chains 155 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054511 restraints weight = 21325.190| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.76 r_work: 0.2689 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9247 Z= 0.252 Angle : 0.643 9.523 12587 Z= 0.327 Chirality : 0.045 0.180 1411 Planarity : 0.004 0.043 1605 Dihedral : 4.985 53.759 1344 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.37 % Allowed : 17.41 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.77 (0.25), residues: 1152 helix: -2.14 (0.60), residues: 53 sheet: 1.09 (0.22), residues: 529 loop : 0.32 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 167 HIS 0.009 0.001 HIS L 189 PHE 0.014 0.001 PHE L 83 TYR 0.027 0.001 TYR B 140 ARG 0.008 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8409 (tp30) REVERT: E 357 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8689 (ttm-80) REVERT: E 386 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8927 (mmmm) REVERT: E 420 ASP cc_start: 0.8804 (m-30) cc_final: 0.8594 (m-30) REVERT: E 462 LYS cc_start: 0.8229 (mttp) cc_final: 0.7963 (mtpm) REVERT: E 516 GLU cc_start: 0.7682 (tp30) cc_final: 0.7351 (pt0) REVERT: H 3 GLN cc_start: 0.8862 (mt0) cc_final: 0.8485 (mp10) REVERT: H 43 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8616 (mmmm) REVERT: H 72 ASP cc_start: 0.7524 (t0) cc_final: 0.6307 (t0) REVERT: H 75 LYS cc_start: 0.9463 (mttp) cc_final: 0.9160 (mtmm) REVERT: H 219 ARG cc_start: 0.9142 (ttt180) cc_final: 0.8835 (tpt170) REVERT: L 17 ASP cc_start: 0.8940 (t0) cc_final: 0.7944 (m-30) REVERT: L 70 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7552 (mp0) REVERT: L 81 ASP cc_start: 0.9265 (m-30) cc_final: 0.8651 (t0) REVERT: L 90 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8568 (pp30) REVERT: L 142 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8577 (mmm-85) REVERT: A 23 LYS cc_start: 0.9081 (tttm) cc_final: 0.8853 (tttm) REVERT: A 62 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8849 (tp40) REVERT: A 82 GLU cc_start: 0.9062 (tt0) cc_final: 0.8405 (tm-30) REVERT: A 89 ASP cc_start: 0.9167 (m-30) cc_final: 0.8618 (p0) REVERT: A 219 LYS cc_start: 0.9323 (mtpt) cc_final: 0.8935 (mmtt) REVERT: B 77 ARG cc_start: 0.8985 (tpp-160) cc_final: 0.8751 (tpp80) REVERT: B 82 ASP cc_start: 0.8444 (m-30) cc_final: 0.7742 (m-30) REVERT: B 105 GLU cc_start: 0.7686 (pp20) cc_final: 0.7451 (pp20) REVERT: B 116 PHE cc_start: 0.8559 (m-10) cc_final: 0.8356 (m-10) REVERT: B 201 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8840 (pp) REVERT: B 210 ASN cc_start: 0.8615 (m-40) cc_final: 0.8301 (p0) REVERT: C 39 GLN cc_start: 0.8923 (tt0) cc_final: 0.8613 (tp40) REVERT: C 43 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8497 (mppt) REVERT: C 45 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: C 65 LYS cc_start: 0.9179 (tttt) cc_final: 0.8888 (tppp) REVERT: C 76 ASN cc_start: 0.9273 (p0) cc_final: 0.8984 (p0) REVERT: C 77 ASN cc_start: 0.9209 (t0) cc_final: 0.8924 (t0) REVERT: C 80 TYR cc_start: 0.8915 (m-80) cc_final: 0.8561 (m-80) REVERT: C 86 LEU cc_start: 0.9187 (mp) cc_final: 0.8929 (mm) REVERT: C 93 ILE cc_start: 0.8755 (mt) cc_final: 0.8456 (mm) outliers start: 24 outliers final: 12 residues processed: 166 average time/residue: 1.3815 time to fit residues: 243.0955 Evaluate side-chains 159 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 97 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.095666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055475 restraints weight = 21329.609| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.74 r_work: 0.2712 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9247 Z= 0.215 Angle : 0.654 11.088 12587 Z= 0.327 Chirality : 0.045 0.176 1411 Planarity : 0.004 0.043 1605 Dihedral : 4.838 53.284 1344 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.27 % Allowed : 17.01 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.82 (0.25), residues: 1152 helix: -2.21 (0.60), residues: 53 sheet: 1.13 (0.22), residues: 528 loop : 0.35 (0.28), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 167 HIS 0.003 0.001 HIS L 189 PHE 0.013 0.001 PHE L 83 TYR 0.020 0.001 TYR B 140 ARG 0.007 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8413 (tp30) REVERT: E 357 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8692 (ttm-80) REVERT: E 386 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8897 (mmmm) REVERT: E 420 ASP cc_start: 0.8791 (m-30) cc_final: 0.8577 (m-30) REVERT: E 462 LYS cc_start: 0.8216 (mttp) cc_final: 0.7940 (mtpp) REVERT: E 516 GLU cc_start: 0.7681 (tp30) cc_final: 0.7308 (pt0) REVERT: H 3 GLN cc_start: 0.8842 (mt0) cc_final: 0.8471 (mp10) REVERT: H 43 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8630 (mmmm) REVERT: H 72 ASP cc_start: 0.7537 (t0) cc_final: 0.6318 (t0) REVERT: H 75 LYS cc_start: 0.9454 (mttp) cc_final: 0.9149 (mtmm) REVERT: H 219 ARG cc_start: 0.9088 (ttt180) cc_final: 0.8745 (tpt-90) REVERT: L 17 ASP cc_start: 0.8950 (t0) cc_final: 0.7946 (m-30) REVERT: L 70 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7521 (mp0) REVERT: L 81 ASP cc_start: 0.9249 (m-30) cc_final: 0.8619 (t0) REVERT: L 90 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8571 (pp30) REVERT: L 105 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7964 (pp20) REVERT: L 142 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8618 (mmm-85) REVERT: A 23 LYS cc_start: 0.9090 (tttm) cc_final: 0.8870 (tttm) REVERT: A 62 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8807 (tp40) REVERT: A 73 ASP cc_start: 0.8443 (t0) cc_final: 0.7881 (t0) REVERT: A 80 TYR cc_start: 0.8711 (m-80) cc_final: 0.8503 (m-10) REVERT: A 82 GLU cc_start: 0.9021 (tt0) cc_final: 0.8416 (tm-30) REVERT: A 87 ARG cc_start: 0.7449 (mpp80) cc_final: 0.7146 (mpp80) REVERT: A 89 ASP cc_start: 0.9172 (m-30) cc_final: 0.8635 (p0) REVERT: A 207 TYR cc_start: 0.8391 (m-80) cc_final: 0.8031 (m-80) REVERT: A 219 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8943 (mmtt) REVERT: B 77 ARG cc_start: 0.9009 (tpp-160) cc_final: 0.8802 (tpp80) REVERT: B 82 ASP cc_start: 0.8461 (m-30) cc_final: 0.7755 (m-30) REVERT: B 201 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8844 (pp) REVERT: B 210 ASN cc_start: 0.8650 (m-40) cc_final: 0.8274 (p0) REVERT: C 39 GLN cc_start: 0.8898 (tt0) cc_final: 0.8608 (tp40) REVERT: C 43 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8517 (mppt) REVERT: C 45 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (mtp85) REVERT: C 65 LYS cc_start: 0.9208 (tttt) cc_final: 0.8928 (tppp) REVERT: C 76 ASN cc_start: 0.9321 (p0) cc_final: 0.9059 (p0) REVERT: C 77 ASN cc_start: 0.9204 (t0) cc_final: 0.8932 (t0) REVERT: C 80 TYR cc_start: 0.8908 (m-80) cc_final: 0.8684 (m-80) REVERT: C 93 ILE cc_start: 0.8733 (mt) cc_final: 0.8454 (mm) outliers start: 23 outliers final: 12 residues processed: 166 average time/residue: 1.4277 time to fit residues: 252.8029 Evaluate side-chains 163 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 chunk 83 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.093137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053138 restraints weight = 21330.955| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.64 r_work: 0.2658 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 9247 Z= 0.479 Angle : 0.714 9.099 12587 Z= 0.363 Chirality : 0.047 0.188 1411 Planarity : 0.005 0.043 1605 Dihedral : 5.055 53.230 1344 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.08 % Allowed : 17.80 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.64 (0.25), residues: 1152 helix: -2.23 (0.61), residues: 53 sheet: 1.02 (0.22), residues: 530 loop : 0.22 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 167 HIS 0.007 0.001 HIS L 189 PHE 0.015 0.002 PHE L 83 TYR 0.044 0.002 TYR B 32 ARG 0.008 0.001 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8423 (tp30) REVERT: E 386 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8895 (mmmm) REVERT: E 420 ASP cc_start: 0.8821 (m-30) cc_final: 0.8614 (m-30) REVERT: E 462 LYS cc_start: 0.8226 (mttp) cc_final: 0.7956 (mtpm) REVERT: E 516 GLU cc_start: 0.7743 (tp30) cc_final: 0.7335 (pt0) REVERT: H 72 ASP cc_start: 0.7706 (t0) cc_final: 0.6493 (t0) REVERT: H 75 LYS cc_start: 0.9444 (mttp) cc_final: 0.9123 (mtmm) REVERT: H 219 ARG cc_start: 0.9114 (ttt180) cc_final: 0.8758 (tpt-90) REVERT: L 17 ASP cc_start: 0.8954 (t0) cc_final: 0.7960 (m-30) REVERT: L 70 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7558 (mp0) REVERT: L 81 ASP cc_start: 0.9274 (m-30) cc_final: 0.8663 (t0) REVERT: L 90 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8661 (pp30) REVERT: L 105 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8048 (pp20) REVERT: L 142 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8534 (mmm-85) REVERT: A 62 GLN cc_start: 0.9403 (mm-40) cc_final: 0.8879 (tp40) REVERT: A 82 GLU cc_start: 0.9086 (tt0) cc_final: 0.8456 (tm-30) REVERT: A 87 ARG cc_start: 0.7585 (mpp80) cc_final: 0.7195 (mpp80) REVERT: A 89 ASP cc_start: 0.9196 (m-30) cc_final: 0.8691 (p0) REVERT: A 167 TRP cc_start: 0.8310 (m100) cc_final: 0.8045 (m-10) REVERT: A 219 LYS cc_start: 0.9305 (mtpt) cc_final: 0.8910 (mmtt) REVERT: B 3 ARG cc_start: 0.8330 (mmp80) cc_final: 0.8123 (mmm160) REVERT: B 70 ASP cc_start: 0.8223 (m-30) cc_final: 0.7856 (t0) REVERT: B 77 ARG cc_start: 0.9070 (tpp-160) cc_final: 0.8830 (tpp80) REVERT: B 82 ASP cc_start: 0.8556 (m-30) cc_final: 0.7844 (m-30) REVERT: B 105 GLU cc_start: 0.7808 (pp20) cc_final: 0.7562 (pp20) REVERT: B 140 TYR cc_start: 0.7304 (t80) cc_final: 0.7017 (t80) REVERT: B 201 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.8867 (pp) REVERT: B 210 ASN cc_start: 0.8671 (m-40) cc_final: 0.8289 (p0) REVERT: C 30 ASP cc_start: 0.8060 (p0) cc_final: 0.7660 (p0) REVERT: C 39 GLN cc_start: 0.8913 (tt0) cc_final: 0.8572 (tp40) REVERT: C 43 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8502 (mppt) REVERT: C 45 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8043 (mtp85) REVERT: C 65 LYS cc_start: 0.9253 (tttt) cc_final: 0.8971 (tppp) REVERT: C 76 ASN cc_start: 0.9287 (p0) cc_final: 0.9011 (p0) REVERT: C 77 ASN cc_start: 0.9192 (t0) cc_final: 0.8959 (t0) REVERT: C 80 TYR cc_start: 0.8973 (m-80) cc_final: 0.8597 (m-80) REVERT: C 85 MET cc_start: 0.8657 (mpp) cc_final: 0.8208 (pmm) REVERT: C 93 ILE cc_start: 0.8829 (mt) cc_final: 0.8566 (mm) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 1.5197 time to fit residues: 256.0077 Evaluate side-chains 159 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 101 HIS A 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.094670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.054631 restraints weight = 21319.144| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.70 r_work: 0.2693 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9247 Z= 0.243 Angle : 0.710 9.603 12587 Z= 0.356 Chirality : 0.046 0.179 1411 Planarity : 0.004 0.042 1605 Dihedral : 4.922 47.729 1344 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.78 % Allowed : 18.89 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.72 (0.25), residues: 1152 helix: -2.27 (0.59), residues: 53 sheet: 1.05 (0.23), residues: 520 loop : 0.31 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 167 HIS 0.005 0.001 HIS A 213 PHE 0.034 0.001 PHE B 116 TYR 0.035 0.001 TYR B 32 ARG 0.008 0.001 ARG C 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8433 (tp30) REVERT: E 357 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8686 (ttm-80) REVERT: E 386 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8889 (mmmm) REVERT: E 420 ASP cc_start: 0.8798 (m-30) cc_final: 0.8578 (m-30) REVERT: E 462 LYS cc_start: 0.8230 (mttp) cc_final: 0.7963 (mtpm) REVERT: E 516 GLU cc_start: 0.7704 (tp30) cc_final: 0.7325 (pt0) REVERT: H 16 GLU cc_start: 0.7725 (tt0) cc_final: 0.7479 (tm-30) REVERT: H 72 ASP cc_start: 0.7635 (t0) cc_final: 0.6411 (t0) REVERT: H 75 LYS cc_start: 0.9432 (mttp) cc_final: 0.9108 (mtmm) REVERT: H 152 LYS cc_start: 0.7812 (tppp) cc_final: 0.7543 (tppp) REVERT: H 219 ARG cc_start: 0.9119 (ttt180) cc_final: 0.8725 (tpt170) REVERT: H 221 GLU cc_start: 0.9156 (pt0) cc_final: 0.8441 (pp20) REVERT: L 17 ASP cc_start: 0.8970 (t0) cc_final: 0.7979 (m-30) REVERT: L 70 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7495 (mp0) REVERT: L 81 ASP cc_start: 0.9282 (m-30) cc_final: 0.8654 (t0) REVERT: L 90 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8575 (pp30) REVERT: L 105 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: L 140 TYR cc_start: 0.7169 (t80) cc_final: 0.6918 (t80) REVERT: L 142 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8596 (mmm-85) REVERT: A 62 GLN cc_start: 0.9379 (mm-40) cc_final: 0.8850 (tp40) REVERT: A 73 ASP cc_start: 0.8597 (t0) cc_final: 0.8161 (OUTLIER) REVERT: A 82 GLU cc_start: 0.9039 (tt0) cc_final: 0.8437 (tm-30) REVERT: A 87 ARG cc_start: 0.7476 (mpp80) cc_final: 0.7165 (mpp80) REVERT: A 89 ASP cc_start: 0.9181 (m-30) cc_final: 0.8683 (p0) REVERT: A 90 ASP cc_start: 0.9137 (m-30) cc_final: 0.8928 (m-30) REVERT: A 98 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7739 (ttp80) REVERT: A 167 TRP cc_start: 0.8272 (m100) cc_final: 0.8021 (m-10) REVERT: A 219 LYS cc_start: 0.9301 (mtpt) cc_final: 0.8905 (mmtt) REVERT: A 223 ARG cc_start: 0.7872 (tpt-90) cc_final: 0.7213 (tpt90) REVERT: A 225 GLU cc_start: 0.8814 (pm20) cc_final: 0.8358 (pm20) REVERT: B 3 ARG cc_start: 0.8349 (mmp80) cc_final: 0.8102 (mmm160) REVERT: B 70 ASP cc_start: 0.8189 (m-30) cc_final: 0.7862 (t0) REVERT: B 77 ARG cc_start: 0.9069 (tpp-160) cc_final: 0.8832 (tpp80) REVERT: B 82 ASP cc_start: 0.8523 (m-30) cc_final: 0.7915 (m-30) REVERT: B 105 GLU cc_start: 0.7805 (pp20) cc_final: 0.7543 (pp20) REVERT: B 140 TYR cc_start: 0.7299 (t80) cc_final: 0.6991 (t80) REVERT: B 201 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8853 (pp) REVERT: B 210 ASN cc_start: 0.8645 (m-40) cc_final: 0.8278 (p0) REVERT: C 39 GLN cc_start: 0.8902 (tt0) cc_final: 0.8590 (tp40) REVERT: C 43 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8487 (mppt) REVERT: C 45 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8028 (mtp85) REVERT: C 65 LYS cc_start: 0.9236 (tttt) cc_final: 0.8965 (tppp) REVERT: C 76 ASN cc_start: 0.9311 (p0) cc_final: 0.9040 (p0) REVERT: C 77 ASN cc_start: 0.9219 (t0) cc_final: 0.8971 (t0) REVERT: C 80 TYR cc_start: 0.8960 (m-80) cc_final: 0.8712 (m-80) REVERT: C 85 MET cc_start: 0.8630 (mpp) cc_final: 0.8273 (pmm) REVERT: C 93 ILE cc_start: 0.8783 (mt) cc_final: 0.8515 (mm) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 1.4670 time to fit residues: 245.9596 Evaluate side-chains 158 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 45 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.095775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.056242 restraints weight = 21357.268| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.65 r_work: 0.2725 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9247 Z= 0.228 Angle : 0.686 9.521 12587 Z= 0.344 Chirality : 0.046 0.173 1411 Planarity : 0.004 0.043 1605 Dihedral : 4.813 42.778 1344 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.78 % Allowed : 18.99 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.87 % Cis-general : 0.00 % 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: 0.78 (0.25), residues: 1152 helix: -2.22 (0.61), residues: 52 sheet: 1.18 (0.23), residues: 500 loop : 0.30 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 167 HIS 0.008 0.001 HIS L 189 PHE 0.031 0.001 PHE B 116 TYR 0.027 0.001 TYR B 32 ARG 0.013 0.001 ARG B 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9167.58 seconds wall clock time: 161 minutes 10.93 seconds (9670.93 seconds total)