Starting phenix.real_space_refine on Tue Mar 11 14:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.map" model { file = "/net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jic_22344/03_2025/7jic_22344.cif" } resolution = 3.8 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= 0.002 sd= 0.034 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 29 5.16 5 C 3770 2.51 5 N 1013 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1625 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 19, 'TRANS': 208} Chain breaks: 4 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1285 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "H" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1601 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1469 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.40, per 1000 atoms: 0.90 Number of scatterers: 5980 At special positions: 0 Unit cell: (61.05, 75.075, 170.775, 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 29 16.00 O 1168 8.00 N 1013 7.00 C 3770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " 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 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 24.2% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'B' and resid 10 through 37 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 58 through 82 Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.827A pdb=" N GLN B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.626A pdb=" N ALA B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 224 removed outlier: 3.747A pdb=" N LYS B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.904A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 182 through 186 removed outlier: 3.696A pdb=" N GLU L 186 " --> pdb=" O LYS L 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 182 through 186' Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.863A pdb=" N GLU A 273 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 4.008A pdb=" N ASP A 32 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA A 34 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU A 36 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 247 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 239 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 74 " --> pdb=" O TRP A 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 84 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 196 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 190 removed outlier: 7.754A pdb=" N LEU A 188 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR A 112 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET A 190 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 114 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N CYS A 97 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.066A pdb=" N LEU A 121 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TRP A 159 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 123 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 160 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.513A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.397A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 108 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.020A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER H 185 " --> pdb=" O PRO H 173 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL H 187 " --> pdb=" O THR H 171 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR H 171 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR H 189 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL H 169 " --> pdb=" O THR H 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.742A pdb=" N THR H 157 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.645A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.570A pdb=" N GLU L 104 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR L 85 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 128 through 135 Processing sheet with id=AB4, first strand: chain 'L' and resid 144 through 149 removed outlier: 3.725A pdb=" N ALA L 192 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS L 193 " --> pdb=" O LYS L 206 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS L 206 " --> pdb=" O CYS L 193 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1948 1.35 - 1.46: 1502 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.81: 41 Bond restraints: 6113 Sorted by residual: bond pdb=" CA ILE A 297 " pdb=" CB ILE A 297 " ideal model delta sigma weight residual 1.540 1.528 0.013 1.25e-02 6.40e+03 1.02e+00 bond pdb=" CA ILE A 306 " pdb=" CB ILE A 306 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 8.84e-01 bond pdb=" CB PRO B 55 " pdb=" CG PRO B 55 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.40e-01 bond pdb=" CA VAL A 304 " pdb=" CB VAL A 304 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.29e-02 6.01e+03 8.24e-01 bond pdb=" CA THR A 292 " pdb=" CB THR A 292 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.70e-02 1.37e+03 7.65e-01 ... (remaining 6108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 8099 1.07 - 2.13: 177 2.13 - 3.20: 64 3.20 - 4.27: 8 4.27 - 5.33: 4 Bond angle restraints: 8352 Sorted by residual: angle pdb=" C THR L 50 " pdb=" CA THR L 50 " pdb=" CB THR L 50 " ideal model delta sigma weight residual 110.42 115.75 -5.33 1.99e+00 2.53e-01 7.18e+00 angle pdb=" N ALA H 16 " pdb=" CA ALA H 16 " pdb=" C ALA H 16 " ideal model delta sigma weight residual 108.34 111.03 -2.69 1.31e+00 5.83e-01 4.22e+00 angle pdb=" N PRO A 203 " pdb=" CA PRO A 203 " pdb=" C PRO A 203 " ideal model delta sigma weight residual 110.70 113.05 -2.35 1.22e+00 6.72e-01 3.70e+00 angle pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 120.60 124.78 -4.18 2.20e+00 2.07e-01 3.62e+00 angle pdb=" CA THR L 50 " pdb=" C THR L 50 " pdb=" N SER L 51 " ideal model delta sigma weight residual 116.84 119.94 -3.10 1.71e+00 3.42e-01 3.29e+00 ... (remaining 8347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.68: 3244 10.68 - 21.36: 230 21.36 - 32.04: 82 32.04 - 42.72: 30 42.72 - 53.40: 6 Dihedral angle restraints: 3592 sinusoidal: 1184 harmonic: 2408 Sorted by residual: dihedral pdb=" SG CYS B 156 " pdb=" CB CYS B 190 " pdb=" SG CYS B 190 " pdb=" CA CYS B 190 " ideal model delta sinusoidal sigma weight residual 79.00 26.09 52.91 1 2.00e+01 2.50e-03 9.53e+00 dihedral pdb=" CA CYS B 157 " pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " pdb=" SG CYS B 175 " ideal model delta sinusoidal sigma weight residual 183.00 131.19 51.81 1 2.00e+01 2.50e-03 9.16e+00 dihedral pdb=" N LYS L 125 " pdb=" CA LYS L 125 " pdb=" CB LYS L 125 " pdb=" CG LYS L 125 " ideal model delta sinusoidal sigma weight residual -60.00 -103.72 43.72 3 1.50e+01 4.44e-03 7.86e+00 ... (remaining 3589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 591 0.026 - 0.052: 237 0.052 - 0.079: 67 0.079 - 0.105: 42 0.105 - 0.131: 24 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL H 92 " pdb=" N VAL H 92 " pdb=" C VAL H 92 " pdb=" CB VAL H 92 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 958 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 203 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 204 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 154 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO H 155 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 155 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 155 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 202 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 203 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.019 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1045 2.77 - 3.30: 5445 3.30 - 3.84: 9764 3.84 - 4.37: 10329 4.37 - 4.90: 18705 Nonbonded interactions: 45288 Sorted by model distance: nonbonded pdb=" OG SER A 53 " pdb=" O SER A 56 " model vdw 2.241 3.040 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 101 " model vdw 2.297 3.040 nonbonded pdb=" O TYR L 185 " pdb=" OH TYR L 191 " model vdw 2.306 3.040 nonbonded pdb=" NE2 GLN A 98 " pdb=" O PRO A 101 " model vdw 2.307 3.120 nonbonded pdb=" O PRO A 203 " pdb=" OG SER A 206 " model vdw 2.310 3.040 ... (remaining 45283 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.400 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6113 Z= 0.134 Angle : 0.447 5.334 8352 Z= 0.237 Chirality : 0.038 0.131 961 Planarity : 0.003 0.043 1076 Dihedral : 9.260 53.399 2014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.97 (0.27), residues: 804 helix: 0.90 (0.34), residues: 196 sheet: -1.81 (0.28), residues: 285 loop : -2.13 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.003 0.001 HIS A 216 PHE 0.008 0.001 PHE A 83 TYR 0.007 0.001 TYR H 103 ARG 0.001 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9556 (mt) cc_final: 0.9303 (tt) REVERT: A 215 THR cc_start: 0.9343 (t) cc_final: 0.8963 (m) REVERT: B 117 ASP cc_start: 0.7363 (p0) cc_final: 0.7141 (p0) REVERT: B 119 ILE cc_start: 0.9289 (mm) cc_final: 0.9073 (mp) REVERT: B 162 LEU cc_start: 0.9325 (tp) cc_final: 0.8914 (tt) REVERT: H 38 LYS cc_start: 0.8842 (tttt) cc_final: 0.8618 (tttm) REVERT: H 151 TYR cc_start: 0.7248 (p90) cc_final: 0.7014 (p90) REVERT: L 43 PRO cc_start: 0.7827 (Cg_endo) cc_final: 0.7596 (Cg_exo) REVERT: L 187 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9077 (mtpp) REVERT: L 206 LYS cc_start: 0.8210 (mmtt) cc_final: 0.6756 (pttt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1835 time to fit residues: 41.4315 Evaluate side-chains 91 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN L 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.115108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082661 restraints weight = 14157.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085380 restraints weight = 8172.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087092 restraints weight = 5777.729| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6113 Z= 0.256 Angle : 0.564 6.731 8352 Z= 0.285 Chirality : 0.041 0.142 961 Planarity : 0.004 0.059 1076 Dihedral : 3.514 15.344 865 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.86 % Favored : 97.01 % Rotamer: Outliers : 1.91 % Allowed : 12.82 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.30), residues: 804 helix: 2.69 (0.35), residues: 182 sheet: -1.17 (0.31), residues: 277 loop : -1.71 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 147 HIS 0.006 0.001 HIS A 218 PHE 0.016 0.001 PHE L 208 TYR 0.011 0.001 TYR L 139 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9564 (mt) cc_final: 0.9292 (tt) REVERT: A 90 GLN cc_start: 0.8393 (pp30) cc_final: 0.8110 (pp30) REVERT: A 215 THR cc_start: 0.9370 (t) cc_final: 0.8971 (m) REVERT: B 117 ASP cc_start: 0.7139 (p0) cc_final: 0.6917 (p0) REVERT: B 119 ILE cc_start: 0.9193 (mm) cc_final: 0.8749 (tp) REVERT: B 162 LEU cc_start: 0.9289 (tp) cc_final: 0.8765 (tt) REVERT: H 200 TYR cc_start: 0.6827 (m-80) cc_final: 0.6445 (m-80) REVERT: H 205 ASN cc_start: 0.8125 (t0) cc_final: 0.7370 (t0) REVERT: L 187 LYS cc_start: 0.9310 (mtpt) cc_final: 0.9062 (mtmm) REVERT: L 198 GLN cc_start: 0.7959 (mp10) cc_final: 0.7621 (pm20) REVERT: L 206 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7220 (mttt) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.1879 time to fit residues: 27.7360 Evaluate side-chains 91 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.0270 chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 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 = 0.3952 r_free = 0.3952 target = 0.114239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.084672 restraints weight = 14267.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085008 restraints weight = 8370.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085744 restraints weight = 6403.974| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6113 Z= 0.211 Angle : 0.531 7.953 8352 Z= 0.265 Chirality : 0.040 0.145 961 Planarity : 0.004 0.047 1076 Dihedral : 3.487 15.831 865 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 14.90 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.22 (0.31), residues: 804 helix: 3.28 (0.36), residues: 182 sheet: -0.95 (0.32), residues: 275 loop : -1.34 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 147 HIS 0.005 0.001 HIS A 218 PHE 0.010 0.001 PHE A 83 TYR 0.010 0.001 TYR A 95 ARG 0.003 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9531 (mt) cc_final: 0.9306 (tt) REVERT: A 215 THR cc_start: 0.9413 (t) cc_final: 0.9032 (m) REVERT: B 48 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6587 (tp30) REVERT: B 117 ASP cc_start: 0.6971 (p0) cc_final: 0.6765 (p0) REVERT: B 119 ILE cc_start: 0.9163 (mm) cc_final: 0.8766 (tp) REVERT: B 132 GLN cc_start: 0.8346 (pp30) cc_final: 0.8026 (pp30) REVERT: B 162 LEU cc_start: 0.9286 (tp) cc_final: 0.8771 (tt) REVERT: H 200 TYR cc_start: 0.6619 (m-80) cc_final: 0.6298 (m-80) REVERT: H 205 ASN cc_start: 0.8147 (t0) cc_final: 0.7623 (t0) REVERT: H 207 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8299 (mmmt) REVERT: L 122 GLU cc_start: 0.8227 (tt0) cc_final: 0.7985 (pt0) REVERT: L 198 GLN cc_start: 0.7885 (mp10) cc_final: 0.7649 (pm20) REVERT: L 206 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7152 (mttt) outliers start: 14 outliers final: 8 residues processed: 104 average time/residue: 0.1881 time to fit residues: 25.7864 Evaluate side-chains 92 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 68 optimal weight: 0.2980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 overall best weight: 1.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.114681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.081003 restraints weight = 14775.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083995 restraints weight = 7849.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.085872 restraints weight = 5358.008| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6113 Z= 0.228 Angle : 0.526 8.267 8352 Z= 0.265 Chirality : 0.040 0.148 961 Planarity : 0.004 0.045 1076 Dihedral : 3.553 15.787 865 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Rotamer: Outliers : 2.08 % Allowed : 15.08 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.06 (0.31), residues: 804 helix: 3.74 (0.35), residues: 181 sheet: -0.82 (0.32), residues: 277 loop : -1.23 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 147 HIS 0.006 0.001 HIS A 218 PHE 0.011 0.001 PHE A 83 TYR 0.017 0.001 TYR A 95 ARG 0.002 0.000 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9526 (mt) cc_final: 0.9299 (tt) REVERT: A 103 SER cc_start: 0.8896 (m) cc_final: 0.8680 (t) REVERT: A 215 THR cc_start: 0.9411 (t) cc_final: 0.8992 (m) REVERT: B 48 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6592 (tp30) REVERT: B 117 ASP cc_start: 0.7239 (p0) cc_final: 0.7007 (p0) REVERT: B 119 ILE cc_start: 0.9203 (mm) cc_final: 0.8827 (tp) REVERT: B 132 GLN cc_start: 0.8485 (pp30) cc_final: 0.8195 (pp30) REVERT: B 162 LEU cc_start: 0.9258 (tp) cc_final: 0.8734 (tt) REVERT: H 150 ASP cc_start: 0.8490 (m-30) cc_final: 0.8240 (m-30) REVERT: H 200 TYR cc_start: 0.6656 (m-80) cc_final: 0.6116 (m-80) REVERT: H 205 ASN cc_start: 0.8223 (t0) cc_final: 0.7550 (t0) REVERT: H 207 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8382 (mmmt) REVERT: H 214 ASP cc_start: 0.8663 (m-30) cc_final: 0.7757 (t0) REVERT: L 104 GLU cc_start: 0.7994 (pt0) cc_final: 0.7748 (pt0) REVERT: L 187 LYS cc_start: 0.9297 (mtpt) cc_final: 0.8857 (mttp) REVERT: L 206 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7230 (mttt) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.1715 time to fit residues: 23.6367 Evaluate side-chains 90 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.113385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079999 restraints weight = 14459.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.082836 restraints weight = 7810.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084751 restraints weight = 5376.225| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6113 Z= 0.250 Angle : 0.528 5.245 8352 Z= 0.269 Chirality : 0.041 0.147 961 Planarity : 0.004 0.043 1076 Dihedral : 3.703 16.551 865 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 14.73 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.23 (0.31), residues: 804 helix: 3.96 (0.34), residues: 182 sheet: -0.76 (0.32), residues: 287 loop : -1.17 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 147 HIS 0.007 0.001 HIS L 197 PHE 0.011 0.001 PHE A 83 TYR 0.016 0.001 TYR A 95 ARG 0.001 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9523 (mt) cc_final: 0.9320 (tt) REVERT: A 215 THR cc_start: 0.9394 (t) cc_final: 0.8972 (m) REVERT: B 117 ASP cc_start: 0.7277 (p0) cc_final: 0.7013 (p0) REVERT: B 119 ILE cc_start: 0.9194 (mm) cc_final: 0.8923 (tp) REVERT: B 132 GLN cc_start: 0.8491 (pp30) cc_final: 0.8234 (pp30) REVERT: B 162 LEU cc_start: 0.9278 (tp) cc_final: 0.8723 (tt) REVERT: H 150 ASP cc_start: 0.8620 (m-30) cc_final: 0.8405 (m-30) REVERT: H 200 TYR cc_start: 0.6650 (m-80) cc_final: 0.6102 (m-80) REVERT: H 205 ASN cc_start: 0.8264 (t0) cc_final: 0.7509 (t0) REVERT: H 214 ASP cc_start: 0.8622 (m-30) cc_final: 0.7749 (t0) REVERT: L 32 MET cc_start: 0.7857 (mmt) cc_final: 0.7638 (mtp) REVERT: L 104 GLU cc_start: 0.7990 (pt0) cc_final: 0.7511 (pt0) REVERT: L 122 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: L 187 LYS cc_start: 0.9292 (mtpt) cc_final: 0.8895 (mttp) REVERT: L 206 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7199 (mttt) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.1704 time to fit residues: 23.8138 Evaluate side-chains 94 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 122 GLU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** 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 = 0.3701 r_free = 0.3701 target = 0.104018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074008 restraints weight = 14025.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076468 restraints weight = 7718.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078024 restraints weight = 5320.700| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 6113 Z= 0.432 Angle : 0.652 8.411 8352 Z= 0.332 Chirality : 0.044 0.280 961 Planarity : 0.004 0.040 1076 Dihedral : 4.269 19.675 865 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 3.29 % Allowed : 16.81 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.04 (0.31), residues: 804 helix: 3.90 (0.35), residues: 184 sheet: -0.96 (0.31), residues: 290 loop : -1.29 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 109 HIS 0.009 0.002 HIS A 218 PHE 0.017 0.002 PHE A 94 TYR 0.013 0.002 TYR H 93 ARG 0.003 0.000 ARG L 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.9522 (mt) cc_final: 0.9307 (tt) REVERT: B 48 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6937 (tp30) REVERT: B 117 ASP cc_start: 0.7380 (p0) cc_final: 0.7079 (p0) REVERT: B 162 LEU cc_start: 0.9316 (tp) cc_final: 0.8754 (tt) REVERT: H 150 ASP cc_start: 0.8815 (m-30) cc_final: 0.8607 (m-30) REVERT: H 200 TYR cc_start: 0.6548 (m-80) cc_final: 0.6018 (m-80) REVERT: H 214 ASP cc_start: 0.8513 (m-30) cc_final: 0.7751 (t0) REVERT: L 104 GLU cc_start: 0.8112 (pt0) cc_final: 0.7693 (pt0) REVERT: L 182 LYS cc_start: 0.8628 (tppt) cc_final: 0.8138 (tppt) REVERT: L 206 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7120 (mttt) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.1700 time to fit residues: 21.9230 Evaluate side-chains 88 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 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 = 0.3926 r_free = 0.3926 target = 0.112692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080461 restraints weight = 14577.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.083178 restraints weight = 8188.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084937 restraints weight = 5730.775| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6113 Z= 0.192 Angle : 0.558 8.083 8352 Z= 0.280 Chirality : 0.041 0.264 961 Planarity : 0.004 0.040 1076 Dihedral : 3.765 17.041 865 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 2.43 % Allowed : 17.33 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.22 (0.31), residues: 804 helix: 3.97 (0.34), residues: 184 sheet: -0.86 (0.32), residues: 281 loop : -1.12 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 147 HIS 0.004 0.001 HIS A 216 PHE 0.009 0.001 PHE A 83 TYR 0.021 0.001 TYR A 95 ARG 0.001 0.000 ARG L 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 THR cc_start: 0.9371 (t) cc_final: 0.8974 (m) REVERT: B 48 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6885 (tp30) REVERT: B 117 ASP cc_start: 0.7348 (p0) cc_final: 0.6997 (p0) REVERT: B 119 ILE cc_start: 0.9293 (mp) cc_final: 0.8867 (tp) REVERT: B 162 LEU cc_start: 0.9251 (tp) cc_final: 0.8678 (tt) REVERT: H 150 ASP cc_start: 0.8700 (m-30) cc_final: 0.8490 (m-30) REVERT: H 200 TYR cc_start: 0.6695 (m-80) cc_final: 0.6127 (m-80) REVERT: H 205 ASN cc_start: 0.8101 (t0) cc_final: 0.7708 (t0) REVERT: H 214 ASP cc_start: 0.8584 (m-30) cc_final: 0.7830 (t0) REVERT: L 77 MET cc_start: 0.6114 (tpt) cc_final: 0.5563 (tpt) REVERT: L 104 GLU cc_start: 0.8047 (pt0) cc_final: 0.7611 (pt0) REVERT: L 121 ASP cc_start: 0.8684 (m-30) cc_final: 0.7958 (p0) REVERT: L 182 LYS cc_start: 0.8608 (tppt) cc_final: 0.8148 (tppt) REVERT: L 206 LYS cc_start: 0.8295 (mmtt) cc_final: 0.7212 (mttt) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.1780 time to fit residues: 23.1449 Evaluate side-chains 88 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 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 = 0.3876 r_free = 0.3876 target = 0.110842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077318 restraints weight = 14719.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.080058 restraints weight = 8035.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.081827 restraints weight = 5573.331| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6113 Z= 0.372 Angle : 0.635 8.372 8352 Z= 0.321 Chirality : 0.043 0.259 961 Planarity : 0.004 0.041 1076 Dihedral : 4.145 19.525 865 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.40 % Rotamer: Outliers : 2.95 % Allowed : 17.85 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.18 (0.31), residues: 804 helix: 4.03 (0.35), residues: 184 sheet: -0.86 (0.31), residues: 291 loop : -1.22 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 147 HIS 0.008 0.002 HIS A 218 PHE 0.015 0.002 PHE A 94 TYR 0.022 0.002 TYR A 95 ARG 0.002 0.000 ARG L 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6836 (tp30) REVERT: B 117 ASP cc_start: 0.7393 (p0) cc_final: 0.7024 (p0) REVERT: B 119 ILE cc_start: 0.9331 (mp) cc_final: 0.8936 (tp) REVERT: B 132 GLN cc_start: 0.8387 (pp30) cc_final: 0.8070 (pp30) REVERT: B 162 LEU cc_start: 0.9301 (tp) cc_final: 0.8721 (tt) REVERT: H 150 ASP cc_start: 0.8838 (m-30) cc_final: 0.8620 (m-30) REVERT: H 200 TYR cc_start: 0.6675 (m-80) cc_final: 0.6063 (m-80) REVERT: H 205 ASN cc_start: 0.8224 (t0) cc_final: 0.7748 (t0) REVERT: L 104 GLU cc_start: 0.8135 (pt0) cc_final: 0.7740 (pt0) REVERT: L 121 ASP cc_start: 0.8662 (m-30) cc_final: 0.7965 (p0) REVERT: L 206 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7131 (mttt) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.1656 time to fit residues: 21.7710 Evaluate side-chains 94 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.110486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078344 restraints weight = 14612.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080904 restraints weight = 8361.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082421 restraints weight = 5910.744| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6113 Z= 0.269 Angle : 0.596 7.097 8352 Z= 0.302 Chirality : 0.042 0.256 961 Planarity : 0.004 0.041 1076 Dihedral : 3.971 18.104 865 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 2.95 % Allowed : 18.02 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.22 (0.31), residues: 804 helix: 4.05 (0.34), residues: 184 sheet: -0.84 (0.31), residues: 290 loop : -1.19 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 147 HIS 0.005 0.001 HIS A 218 PHE 0.011 0.001 PHE A 83 TYR 0.019 0.001 TYR A 95 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8136 (tt) REVERT: B 48 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6850 (tp30) REVERT: B 117 ASP cc_start: 0.7397 (p0) cc_final: 0.6985 (p0) REVERT: B 119 ILE cc_start: 0.9325 (mp) cc_final: 0.8941 (tp) REVERT: B 132 GLN cc_start: 0.8420 (pp30) cc_final: 0.8112 (pp30) REVERT: B 162 LEU cc_start: 0.9280 (tp) cc_final: 0.8695 (tt) REVERT: H 150 ASP cc_start: 0.8763 (m-30) cc_final: 0.8534 (m-30) REVERT: H 198 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: H 205 ASN cc_start: 0.8191 (t0) cc_final: 0.7723 (t0) REVERT: L 77 MET cc_start: 0.6212 (tpt) cc_final: 0.5705 (tpt) REVERT: L 89 GLN cc_start: 0.8464 (tm-30) cc_final: 0.7956 (tm-30) REVERT: L 104 GLU cc_start: 0.8109 (pt0) cc_final: 0.7721 (pt0) REVERT: L 121 ASP cc_start: 0.8627 (m-30) cc_final: 0.7886 (p0) REVERT: L 182 LYS cc_start: 0.8685 (tppt) cc_final: 0.8183 (tppt) REVERT: L 206 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7176 (mttt) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.1594 time to fit residues: 20.7246 Evaluate side-chains 93 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 198 GLN Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 0.3980 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.110405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080624 restraints weight = 14788.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080516 restraints weight = 8777.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080846 restraints weight = 7215.931| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6113 Z= 0.316 Angle : 0.628 8.978 8352 Z= 0.318 Chirality : 0.043 0.254 961 Planarity : 0.004 0.041 1076 Dihedral : 4.094 18.749 865 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.98 % Favored : 95.90 % Rotamer: Outliers : 2.60 % Allowed : 19.06 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.19 (0.31), residues: 804 helix: 4.05 (0.34), residues: 184 sheet: -0.87 (0.31), residues: 290 loop : -1.21 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 147 HIS 0.006 0.001 HIS A 218 PHE 0.012 0.001 PHE A 83 TYR 0.020 0.002 TYR A 95 ARG 0.002 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8048 (tt) REVERT: B 48 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6897 (tp30) REVERT: B 117 ASP cc_start: 0.7443 (p0) cc_final: 0.7015 (p0) REVERT: B 119 ILE cc_start: 0.9332 (mp) cc_final: 0.8985 (tp) REVERT: B 132 GLN cc_start: 0.8447 (pp30) cc_final: 0.8157 (pp30) REVERT: B 162 LEU cc_start: 0.9254 (tp) cc_final: 0.8672 (tt) REVERT: H 150 ASP cc_start: 0.8840 (m-30) cc_final: 0.8630 (m-30) REVERT: H 198 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: H 200 TYR cc_start: 0.6884 (m-80) cc_final: 0.6099 (m-80) REVERT: H 205 ASN cc_start: 0.8106 (t0) cc_final: 0.7730 (t0) REVERT: H 214 ASP cc_start: 0.8544 (m-30) cc_final: 0.7818 (t0) REVERT: L 5 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8492 (p) REVERT: L 77 MET cc_start: 0.6112 (tpt) cc_final: 0.5582 (tpt) REVERT: L 104 GLU cc_start: 0.8133 (pt0) cc_final: 0.7713 (pt0) REVERT: L 121 ASP cc_start: 0.8747 (m-30) cc_final: 0.8094 (p0) REVERT: L 122 GLU cc_start: 0.8167 (pt0) cc_final: 0.7916 (pt0) REVERT: L 182 LYS cc_start: 0.8752 (tppt) cc_final: 0.8252 (tppt) REVERT: L 206 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7196 (mttt) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.1772 time to fit residues: 22.5959 Evaluate side-chains 92 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 198 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079917 restraints weight = 14745.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082885 restraints weight = 7789.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084763 restraints weight = 5287.289| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6113 Z= 0.191 Angle : 0.593 8.428 8352 Z= 0.299 Chirality : 0.042 0.253 961 Planarity : 0.004 0.042 1076 Dihedral : 3.812 17.577 865 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.91 % Allowed : 19.58 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.31), residues: 804 helix: 4.09 (0.34), residues: 184 sheet: -0.76 (0.31), residues: 294 loop : -0.98 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 147 HIS 0.004 0.001 HIS A 216 PHE 0.010 0.001 PHE A 83 TYR 0.015 0.001 TYR A 95 ARG 0.002 0.000 ARG L 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.82 seconds wall clock time: 37 minutes 50.17 seconds (2270.17 seconds total)