Starting phenix.real_space_refine on Fri Nov 15 15:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_16676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_16676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_16676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_16676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cii_16676/11_2024/8cii_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-5513/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: 4.86, per 1000 atoms: 0.54 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: 2.43 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: 1.35 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: 3.22 Time building geometry restraints manager: 2.79 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: 12.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.550 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- 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 : 1.025 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: 1.4589 time to fit residues: 363.6205 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 : 0.973 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 66.627 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 : 1.069 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: 0.8881 (mt-10) cc_final: 0.8278 (tp30) REVERT: E 386 LYS cc_start: 0.9419 (mmmm) cc_final: 0.9166 (mmtp) REVERT: E 390 LEU cc_start: 0.8974 (mt) cc_final: 0.8733 (mp) REVERT: E 462 LYS cc_start: 0.8467 (mttp) cc_final: 0.8169 (mtpm) REVERT: H 3 GLN cc_start: 0.9074 (mt0) cc_final: 0.8682 (mp10) REVERT: H 16 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8088 (mm-30) REVERT: H 72 ASP cc_start: 0.7533 (t0) cc_final: 0.6559 (t0) REVERT: H 75 LYS cc_start: 0.9532 (mttp) cc_final: 0.9325 (mtmm) REVERT: H 129 SER cc_start: 0.8421 (m) cc_final: 0.8105 (p) REVERT: L 17 ASP cc_start: 0.8962 (t0) cc_final: 0.8225 (m-30) REVERT: L 70 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7733 (mp0) REVERT: L 81 ASP cc_start: 0.9067 (m-30) cc_final: 0.8735 (t0) REVERT: L 90 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8867 (pp30) REVERT: L 175 LEU cc_start: 0.8982 (tt) cc_final: 0.8760 (tm) REVERT: A 12 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8912 (mptp) REVERT: A 23 LYS cc_start: 0.9325 (tttm) cc_final: 0.9033 (tttm) REVERT: A 80 TYR cc_start: 0.9090 (m-80) cc_final: 0.8768 (m-10) REVERT: A 82 GLU cc_start: 0.9083 (tt0) cc_final: 0.8506 (tm-30) REVERT: A 130 LYS cc_start: 0.8601 (tttm) cc_final: 0.8239 (tptm) REVERT: A 167 TRP cc_start: 0.8420 (m100) cc_final: 0.8082 (m100) REVERT: A 207 TYR cc_start: 0.8304 (m-80) cc_final: 0.7890 (m-80) REVERT: A 219 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8875 (mmtt) REVERT: B 24 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7968 (ttm110) REVERT: B 82 ASP cc_start: 0.8359 (m-30) cc_final: 0.7566 (m-30) REVERT: B 143 GLU cc_start: 0.7815 (pm20) cc_final: 0.5462 (pm20) REVERT: C 18 LEU cc_start: 0.8874 (tp) cc_final: 0.8659 (tt) REVERT: C 39 GLN cc_start: 0.9432 (tt0) cc_final: 0.8924 (tp40) REVERT: C 43 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9065 (mptt) REVERT: C 76 ASN cc_start: 0.9413 (p0) cc_final: 0.8809 (p0) REVERT: C 77 ASN cc_start: 0.9252 (t0) cc_final: 0.8930 (p0) REVERT: C 80 TYR cc_start: 0.8746 (m-80) cc_final: 0.8260 (m-80) REVERT: C 83 MET cc_start: 0.9250 (mtm) cc_final: 0.8986 (mtm) REVERT: C 93 ILE cc_start: 0.9190 (mt) cc_final: 0.8919 (mm) outliers start: 13 outliers final: 5 residues processed: 187 average time/residue: 1.4285 time to fit residues: 282.5867 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 : 0.971 ------------------------------------------------------------------------------- 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 58 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9247 Z= 0.287 Angle : 0.612 9.081 12587 Z= 0.312 Chirality : 0.045 0.152 1411 Planarity : 0.005 0.048 1605 Dihedral : 5.776 53.303 1344 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.77 % Allowed : 13.45 % Favored : 83.78 % 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: -2.20 (0.59), residues: 58 sheet: 1.07 (0.23), residues: 517 loop : 0.39 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 148 HIS 0.006 0.001 HIS B 198 PHE 0.026 0.001 PHE H 131 TYR 0.041 0.002 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 191 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.068 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: 0.8868 (mt-10) cc_final: 0.8306 (tp30) REVERT: E 462 LYS cc_start: 0.8470 (mttp) cc_final: 0.8162 (mtpm) REVERT: H 3 GLN cc_start: 0.9027 (mt0) cc_final: 0.8618 (mp10) REVERT: H 16 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8082 (mm-30) REVERT: H 43 LYS cc_start: 0.9066 (mmmm) cc_final: 0.8856 (mmmm) REVERT: H 72 ASP cc_start: 0.7715 (t0) cc_final: 0.6556 (t0) REVERT: H 75 LYS cc_start: 0.9532 (mttp) cc_final: 0.9284 (mtmm) REVERT: H 131 PHE cc_start: 0.8115 (m-10) cc_final: 0.7881 (m-10) REVERT: H 219 ARG cc_start: 0.9050 (ttt180) cc_final: 0.8810 (tpt170) REVERT: L 17 ASP cc_start: 0.8996 (t0) cc_final: 0.8165 (m-30) REVERT: L 70 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7754 (mp0) REVERT: L 81 ASP cc_start: 0.9085 (m-30) cc_final: 0.8745 (t0) REVERT: L 90 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8849 (pp30) REVERT: L 142 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8695 (mmm-85) REVERT: A 12 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8861 (mptp) REVERT: A 23 LYS cc_start: 0.9313 (tttm) cc_final: 0.9037 (tttm) REVERT: A 82 GLU cc_start: 0.9059 (tt0) cc_final: 0.8503 (tm-30) REVERT: A 89 ASP cc_start: 0.9093 (m-30) cc_final: 0.8552 (p0) REVERT: A 167 TRP cc_start: 0.8406 (m100) cc_final: 0.8173 (m100) REVERT: A 207 TYR cc_start: 0.8501 (m-80) cc_final: 0.7899 (m-80) REVERT: A 219 LYS cc_start: 0.9228 (mtpt) cc_final: 0.8903 (mmtt) REVERT: A 222 LYS cc_start: 0.8094 (tptp) cc_final: 0.7699 (tmtt) REVERT: B 24 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7952 (ttm110) REVERT: B 82 ASP cc_start: 0.8391 (m-30) cc_final: 0.7707 (m-30) REVERT: C 76 ASN cc_start: 0.9399 (p0) cc_final: 0.9109 (p0) REVERT: C 77 ASN cc_start: 0.9266 (t0) cc_final: 0.8940 (t0) REVERT: C 80 TYR cc_start: 0.8824 (m-80) cc_final: 0.8269 (m-80) REVERT: C 83 MET cc_start: 0.9249 (mtm) cc_final: 0.9008 (mtm) REVERT: C 93 ILE cc_start: 0.9208 (mt) cc_final: 0.8934 (mm) outliers start: 28 outliers final: 12 residues processed: 178 average time/residue: 1.4381 time to fit residues: 271.4935 Evaluate side-chains 162 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 103 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9247 Z= 0.398 Angle : 0.637 8.992 12587 Z= 0.326 Chirality : 0.046 0.171 1411 Planarity : 0.005 0.044 1605 Dihedral : 5.257 54.328 1344 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.26 % Allowed : 13.25 % Favored : 83.48 % 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: 0.61 (0.25), residues: 1152 helix: -2.17 (0.57), residues: 60 sheet: 0.92 (0.22), residues: 538 loop : 0.32 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 148 HIS 0.005 0.001 HIS B 198 PHE 0.014 0.001 PHE H 131 TYR 0.042 0.002 TYR B 140 ARG 0.013 0.001 ARG A 223 *********************** 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 187 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.110 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: 0.8874 (mt-10) cc_final: 0.8338 (tp30) REVERT: E 386 LYS cc_start: 0.9371 (mmmm) cc_final: 0.8914 (mtmp) REVERT: E 462 LYS cc_start: 0.8475 (mttp) cc_final: 0.8166 (mtpm) REVERT: H 3 GLN cc_start: 0.9025 (mt0) cc_final: 0.8624 (mp10) REVERT: H 27 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8958 (m-30) REVERT: H 43 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8851 (mmmm) REVERT: H 72 ASP cc_start: 0.7896 (t0) cc_final: 0.6715 (t0) REVERT: H 75 LYS cc_start: 0.9507 (mttp) cc_final: 0.9217 (mtmm) REVERT: H 131 PHE cc_start: 0.8333 (m-10) cc_final: 0.8068 (m-10) REVERT: L 17 ASP cc_start: 0.9054 (t0) cc_final: 0.8211 (m-30) REVERT: L 70 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7816 (mp0) REVERT: L 81 ASP cc_start: 0.9091 (m-30) cc_final: 0.8738 (t0) REVERT: L 90 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8860 (pp30) REVERT: L 142 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8779 (mmm-85) REVERT: A 12 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8715 (mptp) REVERT: A 23 LYS cc_start: 0.9294 (tttm) cc_final: 0.9047 (tttm) REVERT: A 62 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8683 (tp40) REVERT: A 82 GLU cc_start: 0.9055 (tt0) cc_final: 0.8504 (tm-30) REVERT: A 89 ASP cc_start: 0.9140 (m-30) cc_final: 0.8629 (p0) REVERT: A 207 TYR cc_start: 0.8271 (m-80) cc_final: 0.7803 (m-80) REVERT: A 219 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8903 (mmtt) REVERT: A 222 LYS cc_start: 0.7925 (tptp) cc_final: 0.7489 (tptp) REVERT: A 223 ARG cc_start: 0.8596 (ttp80) cc_final: 0.7948 (ttp80) REVERT: B 24 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7870 (ttm110) REVERT: B 82 ASP cc_start: 0.8483 (m-30) cc_final: 0.7777 (m-30) REVERT: B 105 GLU cc_start: 0.8219 (pp20) cc_final: 0.7952 (pp20) REVERT: C 30 ASP cc_start: 0.8570 (p0) cc_final: 0.8267 (p0) REVERT: C 39 GLN cc_start: 0.9287 (tt0) cc_final: 0.8919 (tp40) REVERT: C 45 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8467 (mtp85) REVERT: C 65 LYS cc_start: 0.8940 (tppp) cc_final: 0.8733 (tppp) REVERT: C 76 ASN cc_start: 0.9393 (p0) cc_final: 0.9105 (p0) REVERT: C 77 ASN cc_start: 0.9270 (t0) cc_final: 0.8962 (t0) REVERT: C 80 TYR cc_start: 0.8938 (m-80) cc_final: 0.8359 (m-80) REVERT: C 85 MET cc_start: 0.8537 (mpp) cc_final: 0.8248 (mpp) REVERT: C 93 ILE cc_start: 0.9300 (mt) cc_final: 0.8972 (mm) outliers start: 33 outliers final: 13 residues processed: 174 average time/residue: 1.4430 time to fit residues: 266.3271 Evaluate side-chains 162 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 11 LEU 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 B residue 33 LEU Chi-restraints excluded: chain B residue 185 ASP 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 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3291 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= 0.218 Angle : 0.614 9.686 12587 Z= 0.312 Chirality : 0.045 0.187 1411 Planarity : 0.005 0.045 1605 Dihedral : 4.992 53.500 1344 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.27 % Allowed : 15.23 % Favored : 82.49 % 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: 0.71 (0.25), residues: 1152 helix: -2.07 (0.57), residues: 60 sheet: 1.05 (0.22), residues: 523 loop : 0.32 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 167 HIS 0.002 0.001 HIS A 213 PHE 0.015 0.001 PHE B 116 TYR 0.028 0.001 TYR B 140 ARG 0.008 0.001 ARG B 211 *********************** 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 180 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8335 (tp30) REVERT: E 462 LYS cc_start: 0.8476 (mttp) cc_final: 0.8160 (mtpm) REVERT: H 3 GLN cc_start: 0.8989 (mt0) cc_final: 0.8606 (mp10) REVERT: H 43 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8846 (mmmm) REVERT: H 72 ASP cc_start: 0.7892 (t0) cc_final: 0.6632 (t0) REVERT: H 75 LYS cc_start: 0.9505 (mttp) cc_final: 0.9220 (mtmm) REVERT: H 219 ARG cc_start: 0.9046 (ttt180) cc_final: 0.8787 (tpt-90) REVERT: L 17 ASP cc_start: 0.9058 (t0) cc_final: 0.8227 (m-30) REVERT: L 70 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7728 (mp0) REVERT: L 81 ASP cc_start: 0.9073 (m-30) cc_final: 0.8718 (t0) REVERT: L 90 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8853 (pp30) REVERT: L 142 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8622 (mmm-85) REVERT: A 23 LYS cc_start: 0.9285 (tttm) cc_final: 0.9021 (tttm) REVERT: A 62 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8654 (tp40) REVERT: A 82 GLU cc_start: 0.8974 (tt0) cc_final: 0.8470 (tm-30) REVERT: A 89 ASP cc_start: 0.9109 (m-30) cc_final: 0.8652 (p0) REVERT: A 205 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: A 219 LYS cc_start: 0.9257 (mtpt) cc_final: 0.8935 (mmtt) REVERT: B 77 ARG cc_start: 0.8692 (tpp-160) cc_final: 0.8484 (tpp-160) REVERT: B 82 ASP cc_start: 0.8506 (m-30) cc_final: 0.7748 (m-30) REVERT: C 39 GLN cc_start: 0.9191 (tt0) cc_final: 0.8778 (tp40) REVERT: C 45 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8445 (mtp85) REVERT: C 65 LYS cc_start: 0.8907 (tppp) cc_final: 0.8682 (tppp) REVERT: C 76 ASN cc_start: 0.9400 (p0) cc_final: 0.9149 (p0) REVERT: C 77 ASN cc_start: 0.9273 (t0) cc_final: 0.8945 (t0) REVERT: C 80 TYR cc_start: 0.8929 (m-80) cc_final: 0.8605 (m-80) REVERT: C 93 ILE cc_start: 0.9227 (mt) cc_final: 0.8863 (mm) outliers start: 23 outliers final: 9 residues processed: 171 average time/residue: 1.4835 time to fit residues: 268.3158 Evaluate side-chains 152 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 140 TYR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 205 GLN 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 100 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9247 Z= 0.195 Angle : 0.620 9.617 12587 Z= 0.314 Chirality : 0.045 0.224 1411 Planarity : 0.005 0.043 1605 Dihedral : 4.869 53.137 1344 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.27 % Allowed : 16.91 % 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: 0.73 (0.25), residues: 1152 helix: -2.38 (0.54), residues: 60 sheet: 1.08 (0.22), residues: 525 loop : 0.36 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 167 HIS 0.003 0.001 HIS L 198 PHE 0.020 0.001 PHE B 118 TYR 0.027 0.001 TYR B 140 ARG 0.011 0.001 ARG B 24 *********************** 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: 23 poor density : 152 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8331 (tp30) REVERT: E 357 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8555 (ttm-80) REVERT: E 386 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8985 (mmmm) REVERT: E 420 ASP cc_start: 0.8821 (m-30) cc_final: 0.8553 (m-30) REVERT: E 462 LYS cc_start: 0.8472 (mttp) cc_final: 0.8127 (mtpp) REVERT: H 3 GLN cc_start: 0.8965 (mt0) cc_final: 0.8603 (mp10) REVERT: H 43 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8852 (mmmm) REVERT: H 72 ASP cc_start: 0.7868 (t0) cc_final: 0.6577 (t0) REVERT: H 75 LYS cc_start: 0.9498 (mttp) cc_final: 0.9209 (mtmm) REVERT: H 219 ARG cc_start: 0.9044 (ttt180) cc_final: 0.8825 (tpt170) REVERT: L 17 ASP cc_start: 0.9065 (t0) cc_final: 0.8231 (m-30) REVERT: L 70 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7714 (mp0) REVERT: L 81 ASP cc_start: 0.9067 (m-30) cc_final: 0.8712 (t0) REVERT: L 90 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8847 (pp30) REVERT: L 142 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8748 (mmm-85) REVERT: A 23 LYS cc_start: 0.9292 (tttm) cc_final: 0.9027 (tttm) REVERT: A 62 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8610 (tp40) REVERT: A 73 ASP cc_start: 0.8695 (t0) cc_final: 0.8149 (t0) REVERT: A 80 TYR cc_start: 0.9045 (m-80) cc_final: 0.8806 (m-10) REVERT: A 82 GLU cc_start: 0.8863 (tt0) cc_final: 0.8389 (tm-30) REVERT: A 89 ASP cc_start: 0.9105 (m-30) cc_final: 0.8666 (p0) REVERT: A 205 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: A 223 ARG cc_start: 0.8468 (tmm160) cc_final: 0.8158 (tmm160) REVERT: B 82 ASP cc_start: 0.8502 (m-30) cc_final: 0.7678 (m-30) REVERT: B 201 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8777 (pp) REVERT: B 210 ASN cc_start: 0.8582 (m-40) cc_final: 0.8185 (p0) REVERT: C 39 GLN cc_start: 0.9162 (tt0) cc_final: 0.8780 (tp40) REVERT: C 45 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8431 (mtp85) REVERT: C 65 LYS cc_start: 0.8912 (tppp) cc_final: 0.8679 (tppp) REVERT: C 76 ASN cc_start: 0.9408 (p0) cc_final: 0.9130 (p0) REVERT: C 77 ASN cc_start: 0.9286 (t0) cc_final: 0.8955 (t0) REVERT: C 80 TYR cc_start: 0.8921 (m-80) cc_final: 0.8545 (m-80) REVERT: C 93 ILE cc_start: 0.9159 (mt) cc_final: 0.8789 (mm) outliers start: 23 outliers final: 10 residues processed: 168 average time/residue: 1.3986 time to fit residues: 249.2167 Evaluate side-chains 154 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 142 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN 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 45 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 9247 Z= 0.474 Angle : 0.692 9.249 12587 Z= 0.353 Chirality : 0.047 0.161 1411 Planarity : 0.005 0.042 1605 Dihedral : 5.066 52.918 1344 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.87 % Allowed : 17.31 % Favored : 79.82 % 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: 0.60 (0.25), residues: 1152 helix: -2.18 (0.60), residues: 53 sheet: 0.98 (0.22), residues: 537 loop : 0.19 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 167 HIS 0.008 0.001 HIS L 189 PHE 0.019 0.002 PHE B 118 TYR 0.028 0.002 TYR B 140 ARG 0.011 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 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8376 (tp30) REVERT: E 386 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8999 (mmmm) REVERT: E 420 ASP cc_start: 0.8849 (m-30) cc_final: 0.8639 (m-30) REVERT: E 462 LYS cc_start: 0.8474 (mttp) cc_final: 0.8148 (mtpm) REVERT: E 516 GLU cc_start: 0.7661 (pt0) cc_final: 0.7091 (pp20) REVERT: H 27 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8949 (m-30) REVERT: H 43 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8870 (mmmm) REVERT: H 72 ASP cc_start: 0.7981 (t0) cc_final: 0.6685 (t0) REVERT: H 75 LYS cc_start: 0.9489 (mttp) cc_final: 0.9194 (mtmm) REVERT: H 219 ARG cc_start: 0.9025 (ttt180) cc_final: 0.8802 (tpt170) REVERT: L 17 ASP cc_start: 0.9116 (t0) cc_final: 0.8250 (m-30) REVERT: L 70 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7790 (mp0) REVERT: L 81 ASP cc_start: 0.9091 (m-30) cc_final: 0.8696 (t0) REVERT: L 90 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8950 (pp30) REVERT: L 140 TYR cc_start: 0.7818 (t80) cc_final: 0.7614 (t80) REVERT: L 142 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8756 (mmm-85) REVERT: A 23 LYS cc_start: 0.9252 (tttm) cc_final: 0.9008 (tttm) REVERT: A 62 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8679 (tp40) REVERT: A 82 GLU cc_start: 0.8949 (tt0) cc_final: 0.8460 (tm-30) REVERT: A 89 ASP cc_start: 0.9152 (m-30) cc_final: 0.8726 (p0) REVERT: A 205 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: A 219 LYS cc_start: 0.9287 (mtpt) cc_final: 0.8956 (mmtt) REVERT: B 82 ASP cc_start: 0.8568 (m-30) cc_final: 0.7897 (m-30) REVERT: B 105 GLU cc_start: 0.7929 (pp20) cc_final: 0.7709 (pp20) REVERT: B 201 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 210 ASN cc_start: 0.8666 (m-40) cc_final: 0.8285 (p0) REVERT: C 30 ASP cc_start: 0.8647 (p0) cc_final: 0.8301 (p0) REVERT: C 39 GLN cc_start: 0.9169 (tt0) cc_final: 0.8711 (tp40) REVERT: C 43 LYS cc_start: 0.9246 (mtmm) cc_final: 0.8656 (mppt) REVERT: C 65 LYS cc_start: 0.9006 (tppp) cc_final: 0.8764 (tppp) REVERT: C 76 ASN cc_start: 0.9401 (p0) cc_final: 0.9088 (p0) REVERT: C 93 ILE cc_start: 0.9274 (mt) cc_final: 0.8908 (mm) outliers start: 29 outliers final: 15 residues processed: 166 average time/residue: 1.3864 time to fit residues: 244.2687 Evaluate side-chains 159 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 142 ARG Chi-restraints excluded: chain L residue 185 ASP Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 163 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 124 GLN C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9247 Z= 0.235 Angle : 0.663 9.617 12587 Z= 0.335 Chirality : 0.045 0.171 1411 Planarity : 0.005 0.052 1605 Dihedral : 4.870 45.695 1344 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.47 % Allowed : 18.20 % 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: 0.63 (0.25), residues: 1152 helix: -2.27 (0.60), residues: 52 sheet: 1.02 (0.23), residues: 528 loop : 0.21 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 167 HIS 0.003 0.001 HIS L 189 PHE 0.013 0.001 PHE L 83 TYR 0.027 0.001 TYR B 140 ARG 0.009 0.001 ARG A 223 *********************** 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: 25 poor density : 150 time to evaluate : 1.161 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: 0.8849 (mt-10) cc_final: 0.8371 (tp30) REVERT: E 386 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8939 (mmmm) REVERT: E 420 ASP cc_start: 0.8821 (m-30) cc_final: 0.8615 (m-30) REVERT: E 462 LYS cc_start: 0.8470 (mttp) cc_final: 0.8140 (mtpm) REVERT: E 516 GLU cc_start: 0.7404 (pt0) cc_final: 0.6953 (pp20) REVERT: H 72 ASP cc_start: 0.7971 (t0) cc_final: 0.6687 (t0) REVERT: H 75 LYS cc_start: 0.9471 (mttp) cc_final: 0.9159 (mtmm) REVERT: H 219 ARG cc_start: 0.9013 (ttt180) cc_final: 0.8742 (tpt-90) REVERT: L 17 ASP cc_start: 0.9093 (t0) cc_final: 0.8245 (m-30) REVERT: L 70 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7705 (mp0) REVERT: L 81 ASP cc_start: 0.9084 (m-30) cc_final: 0.8705 (t0) REVERT: L 90 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8858 (pp30) REVERT: A 23 LYS cc_start: 0.9238 (tttm) cc_final: 0.8968 (tttm) REVERT: A 62 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8605 (tp40) REVERT: A 73 ASP cc_start: 0.8738 (t0) cc_final: 0.8284 (OUTLIER) REVERT: A 82 GLU cc_start: 0.8831 (tt0) cc_final: 0.8417 (tm-30) REVERT: A 87 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7482 (mpp80) REVERT: A 89 ASP cc_start: 0.9144 (m-30) cc_final: 0.8756 (p0) REVERT: A 205 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: A 207 TYR cc_start: 0.8016 (m-80) cc_final: 0.7182 (m-80) REVERT: A 219 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8979 (mmtt) REVERT: B 3 ARG cc_start: 0.8371 (mmp80) cc_final: 0.8096 (mmm160) REVERT: B 70 ASP cc_start: 0.8440 (m-30) cc_final: 0.8125 (t0) REVERT: B 82 ASP cc_start: 0.8498 (m-30) cc_final: 0.7851 (m-30) REVERT: B 201 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8841 (pp) REVERT: B 210 ASN cc_start: 0.8678 (m-40) cc_final: 0.8306 (p0) REVERT: C 39 GLN cc_start: 0.9158 (tt0) cc_final: 0.8736 (tp40) REVERT: C 43 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8641 (mppt) REVERT: C 65 LYS cc_start: 0.8976 (tppp) cc_final: 0.8744 (tppp) REVERT: C 76 ASN cc_start: 0.9536 (p0) cc_final: 0.9217 (p0) REVERT: C 84 ASN cc_start: 0.8524 (m-40) cc_final: 0.8284 (m-40) REVERT: C 93 ILE cc_start: 0.9150 (mt) cc_final: 0.8821 (mm) outliers start: 25 outliers final: 13 residues processed: 168 average time/residue: 1.3842 time to fit residues: 246.9804 Evaluate side-chains 159 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN 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 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 9247 Z= 0.552 Angle : 0.746 11.696 12587 Z= 0.380 Chirality : 0.048 0.199 1411 Planarity : 0.005 0.055 1605 Dihedral : 5.162 45.037 1344 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 18.10 % Favored : 79.13 % 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: 0.39 (0.25), residues: 1152 helix: -2.26 (0.60), residues: 53 sheet: 0.88 (0.22), residues: 537 loop : -0.01 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 167 HIS 0.005 0.001 HIS A 108 PHE 0.045 0.002 PHE C 68 TYR 0.044 0.002 TYR B 32 ARG 0.010 0.001 ARG A 223 *********************** 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 173 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8393 (tp30) REVERT: E 386 LYS cc_start: 0.9309 (mmmm) cc_final: 0.8983 (mmmm) REVERT: E 420 ASP cc_start: 0.8844 (m-30) cc_final: 0.8643 (m-30) REVERT: E 462 LYS cc_start: 0.8463 (mttp) cc_final: 0.8142 (mtpm) REVERT: E 516 GLU cc_start: 0.7497 (pt0) cc_final: 0.7013 (pp20) REVERT: H 27 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (m-30) REVERT: H 72 ASP cc_start: 0.8123 (t0) cc_final: 0.7018 (t0) REVERT: H 75 LYS cc_start: 0.9470 (mttp) cc_final: 0.9220 (mtmm) REVERT: H 219 ARG cc_start: 0.9027 (ttt180) cc_final: 0.8710 (tpt-90) REVERT: L 17 ASP cc_start: 0.9118 (t0) cc_final: 0.8228 (m-30) REVERT: L 70 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7800 (mp0) REVERT: L 81 ASP cc_start: 0.9079 (m-30) cc_final: 0.8723 (t0) REVERT: L 90 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8947 (pp30) REVERT: A 23 LYS cc_start: 0.9231 (tttm) cc_final: 0.9020 (tttm) REVERT: A 62 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8648 (tp-100) REVERT: A 82 GLU cc_start: 0.8952 (tt0) cc_final: 0.8467 (tm-30) REVERT: A 87 ARG cc_start: 0.7895 (mpp80) cc_final: 0.7587 (mpp80) REVERT: A 89 ASP cc_start: 0.9162 (m-30) cc_final: 0.8794 (p0) REVERT: A 205 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: A 219 LYS cc_start: 0.9264 (mtpt) cc_final: 0.8919 (mmtt) REVERT: B 70 ASP cc_start: 0.8436 (m-30) cc_final: 0.8100 (t0) REVERT: B 82 ASP cc_start: 0.8637 (m-30) cc_final: 0.8042 (m-30) REVERT: B 105 GLU cc_start: 0.7993 (pp20) cc_final: 0.7753 (pp20) REVERT: B 201 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8867 (pp) REVERT: B 210 ASN cc_start: 0.8654 (m-40) cc_final: 0.8239 (p0) REVERT: C 30 ASP cc_start: 0.8652 (p0) cc_final: 0.8285 (p0) REVERT: C 39 GLN cc_start: 0.9187 (tt0) cc_final: 0.8690 (tp40) REVERT: C 43 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8659 (mppt) REVERT: C 65 LYS cc_start: 0.9099 (tppp) cc_final: 0.8888 (tppp) REVERT: C 76 ASN cc_start: 0.9513 (p0) cc_final: 0.9234 (p0) REVERT: C 93 ILE cc_start: 0.9251 (mt) cc_final: 0.8949 (mm) outliers start: 28 outliers final: 15 residues processed: 161 average time/residue: 1.4896 time to fit residues: 253.9588 Evaluate side-chains 157 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 ASP 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 H residue 220 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 205 GLN 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 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS C 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9247 Z= 0.244 Angle : 0.715 9.658 12587 Z= 0.362 Chirality : 0.047 0.306 1411 Planarity : 0.005 0.059 1605 Dihedral : 5.005 43.466 1344 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 19.49 % Favored : 78.64 % 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: 0.47 (0.25), residues: 1152 helix: -2.33 (0.58), residues: 52 sheet: 0.94 (0.23), residues: 528 loop : 0.06 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 167 HIS 0.004 0.001 HIS L 189 PHE 0.063 0.002 PHE C 68 TYR 0.034 0.002 TYR B 32 ARG 0.012 0.001 ARG A 223 ********************** 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 167 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 340 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8387 (tp30) REVERT: E 357 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8601 (ttm-80) REVERT: E 386 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8964 (mmmm) REVERT: E 420 ASP cc_start: 0.8820 (m-30) cc_final: 0.8607 (m-30) REVERT: E 462 LYS cc_start: 0.8469 (mttp) cc_final: 0.8143 (mtpm) REVERT: E 516 GLU cc_start: 0.7436 (pt0) cc_final: 0.6981 (pp20) REVERT: H 16 GLU cc_start: 0.7887 (tt0) cc_final: 0.7597 (tm-30) REVERT: H 72 ASP cc_start: 0.8057 (t0) cc_final: 0.6919 (t0) REVERT: H 75 LYS cc_start: 0.9452 (mttp) cc_final: 0.9192 (mtmm) REVERT: H 152 LYS cc_start: 0.8173 (tppp) cc_final: 0.7837 (tppp) REVERT: H 219 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8671 (tpt170) REVERT: H 221 GLU cc_start: 0.9125 (pt0) cc_final: 0.8405 (pp20) REVERT: L 17 ASP cc_start: 0.9102 (t0) cc_final: 0.8252 (m-30) REVERT: L 70 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7710 (mp0) REVERT: L 81 ASP cc_start: 0.9055 (m-30) cc_final: 0.8700 (t0) REVERT: L 90 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8878 (pp30) REVERT: L 142 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8557 (mmm-85) REVERT: A 23 LYS cc_start: 0.9228 (tttm) cc_final: 0.8944 (tttm) REVERT: A 62 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8646 (tp40) REVERT: A 73 ASP cc_start: 0.8866 (t0) cc_final: 0.8435 (t0) REVERT: A 82 GLU cc_start: 0.8844 (tt0) cc_final: 0.8427 (tm-30) REVERT: A 87 ARG cc_start: 0.7847 (mpp80) cc_final: 0.7507 (mpp80) REVERT: A 89 ASP cc_start: 0.9108 (m-30) cc_final: 0.8772 (p0) REVERT: A 205 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: A 219 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8933 (mmtt) REVERT: B 3 ARG cc_start: 0.8345 (mmp80) cc_final: 0.8130 (mmm160) REVERT: B 70 ASP cc_start: 0.8408 (m-30) cc_final: 0.8105 (t0) REVERT: B 82 ASP cc_start: 0.8591 (m-30) cc_final: 0.7981 (m-30) REVERT: B 105 GLU cc_start: 0.8009 (pp20) cc_final: 0.7721 (pp20) REVERT: B 140 TYR cc_start: 0.7682 (t80) cc_final: 0.7402 (t80) REVERT: B 201 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8871 (pp) REVERT: B 210 ASN cc_start: 0.8648 (m-40) cc_final: 0.8210 (p0) REVERT: C 39 GLN cc_start: 0.9171 (tt0) cc_final: 0.8748 (tp40) REVERT: C 43 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8629 (mppt) REVERT: C 65 LYS cc_start: 0.9034 (tppp) cc_final: 0.8781 (tppp) REVERT: C 76 ASN cc_start: 0.9550 (p0) cc_final: 0.9233 (p0) REVERT: C 85 MET cc_start: 0.8291 (mpp) cc_final: 0.8073 (pmm) REVERT: C 93 ILE cc_start: 0.9176 (mt) cc_final: 0.8844 (mm) outliers start: 19 outliers final: 12 residues processed: 161 average time/residue: 1.3711 time to fit residues: 234.2620 Evaluate side-chains 158 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 205 GLN 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 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.056017 restraints weight = 20900.838| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.64 r_work: 0.2731 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9247 Z= 0.241 Angle : 0.717 10.827 12587 Z= 0.360 Chirality : 0.046 0.190 1411 Planarity : 0.005 0.043 1605 Dihedral : 4.922 42.650 1344 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.78 % Allowed : 20.08 % Favored : 78.14 % 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: 0.58 (0.25), residues: 1152 helix: -2.24 (0.60), residues: 52 sheet: 1.00 (0.23), residues: 526 loop : 0.15 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 167 HIS 0.008 0.001 HIS L 189 PHE 0.040 0.001 PHE C 68 TYR 0.034 0.001 TYR L 140 ARG 0.010 0.001 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4705.39 seconds wall clock time: 85 minutes 40.59 seconds (5140.59 seconds total)