Starting phenix.real_space_refine on Thu Jul 24 10:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.map" model { file = "/net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pwc_20505/07_2025/6pwc_20505.cif" } resolution = 4.9 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= 0.003 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 25 5.16 5 C 3562 2.51 5 N 1065 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5879 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1824 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 10, 'TRANS': 312} Chain breaks: 2 Unresolved non-hydrogen bonds: 779 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 677 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 9, 'TYR:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 4, 'ASP:plan': 8, 'PHE:plan': 17, 'GLU:plan': 6, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 475 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 27 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1935 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 324} Unresolved non-hydrogen bonds: 863 Unresolved non-hydrogen angles: 1078 Unresolved non-hydrogen dihedrals: 721 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 21, 'TYR:plan': 11, 'ASN:plan1': 14, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 522 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1072 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 184} Chain breaks: 3 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 14, 'ASN:plan1': 7, 'TRP:plan': 5, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 307 Chain: "L" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1021 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 278 Time building chain proxies: 4.15, per 1000 atoms: 0.71 Number of scatterers: 5879 At special positions: 0 Unit cell: (161.867, 106.193, 90.728, 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 25 16.00 O 1227 8.00 N 1065 7.00 C 3562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS H 59 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 1.42 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 30.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 98 through 129 Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 137 through 172 Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.959A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 269 removed outlier: 3.694A pdb=" N VAL R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG R 268 " --> pdb=" O THR R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 329 removed outlier: 3.848A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.197A pdb=" N ARG R 323 " --> pdb=" O TYR R 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 329 " --> pdb=" O MET R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 4.160A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 383 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.775A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 185 through 190 removed outlier: 4.252A pdb=" N LYS L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 208 through 211 Processing sheet with id=AA2, first strand: chain 'R' and resid 411 through 413 removed outlier: 3.629A pdb=" N ASN R 411 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR R 413 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.898A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 4.036A pdb=" N PHE A 75 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 53 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77 removed outlier: 4.036A pdb=" N PHE A 75 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AA8, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.065A pdb=" N TYR A 208 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 330 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL A 228 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.888A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 15 Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.927A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 179 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB5, first strand: chain 'H' and resid 173 through 175 Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.236A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.105A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN L 159 " --> pdb=" O THR L 181 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1182 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: 1.91 Time building geometry restraints manager: 1.70 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: 2088 1.34 - 1.46: 1158 1.46 - 1.58: 2664 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 5935 Sorted by residual: bond pdb=" C LYS A 355 " pdb=" N PRO A 356 " ideal model delta sigma weight residual 1.341 1.376 -0.035 1.60e-02 3.91e+03 4.87e+00 bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.52e+00 bond pdb=" C VAL R 201 " pdb=" N PRO R 202 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.35e+00 bond pdb=" C LEU R 317 " pdb=" N PRO R 318 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.25e-02 6.40e+03 2.98e+00 bond pdb=" CA VAL R 201 " pdb=" C VAL R 201 " ideal model delta sigma weight residual 1.523 1.537 -0.014 9.20e-03 1.18e+04 2.31e+00 ... (remaining 5930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 8005 1.57 - 3.14: 236 3.14 - 4.70: 21 4.70 - 6.27: 12 6.27 - 7.84: 6 Bond angle restraints: 8280 Sorted by residual: angle pdb=" C ALA R 200 " pdb=" N VAL R 201 " pdb=" CA VAL R 201 " ideal model delta sigma weight residual 120.33 125.09 -4.76 8.00e-01 1.56e+00 3.54e+01 angle pdb=" CA VAL R 201 " pdb=" C VAL R 201 " pdb=" N PRO R 202 " ideal model delta sigma weight residual 120.83 122.82 -1.99 6.10e-01 2.69e+00 1.07e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA LYS A 95 " pdb=" C LYS A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 118.44 123.01 -4.57 1.59e+00 3.96e-01 8.25e+00 angle pdb=" CA GLY A 316 " pdb=" C GLY A 316 " pdb=" N ILE A 317 " ideal model delta sigma weight residual 114.62 118.23 -3.61 1.26e+00 6.30e-01 8.20e+00 ... (remaining 8275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.22: 3517 12.22 - 24.43: 24 24.43 - 36.65: 2 36.65 - 48.87: 3 48.87 - 61.08: 2 Dihedral angle restraints: 3548 sinusoidal: 501 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 154.08 -61.08 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS H 59 " pdb=" CB CYS H 59 " ideal model delta sinusoidal sigma weight residual -86.00 -32.21 -53.79 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA TRP H 113 " pdb=" C TRP H 113 " pdb=" N GLY H 114 " pdb=" CA GLY H 114 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 765 0.036 - 0.072: 268 0.072 - 0.109: 88 0.109 - 0.145: 48 0.145 - 0.181: 3 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CA THR R 115 " pdb=" N THR R 115 " pdb=" C THR R 115 " pdb=" CB THR R 115 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA MET R 120 " pdb=" N MET R 120 " pdb=" C MET R 120 " pdb=" CB MET R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA LEU R 317 " pdb=" N LEU R 317 " pdb=" C LEU R 317 " pdb=" CB LEU R 317 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1169 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 225 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO R 226 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 267 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C VAL R 267 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL R 267 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG R 268 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 144 " 0.018 2.00e-02 2.50e+03 1.23e-02 3.03e+00 pdb=" CG TYR R 144 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR R 144 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR R 144 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR R 144 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 144 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR R 144 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 144 " -0.001 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 1987 2.86 - 3.37: 5096 3.37 - 3.88: 8881 3.88 - 4.39: 7784 4.39 - 4.90: 15405 Nonbonded interactions: 39153 Sorted by model distance: nonbonded pdb=" O ASN R 240 " pdb=" OG SER R 244 " model vdw 2.345 3.040 nonbonded pdb=" O TYR R 354 " pdb=" OG1 THR R 358 " model vdw 2.376 3.040 nonbonded pdb=" O HIS H 210 " pdb=" N ASN H 214 " model vdw 2.380 3.120 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.393 3.040 nonbonded pdb=" O ALA A 263 " pdb=" OG SER A 266 " model vdw 2.401 3.040 ... (remaining 39148 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: 1.100 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.003 0.045 5939 Z= 0.180 Angle : 0.668 7.838 8288 Z= 0.392 Chirality : 0.046 0.181 1172 Planarity : 0.006 0.046 1111 Dihedral : 4.676 21.029 1536 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -0.09 (0.24), residues: 1031 helix: 0.54 (0.27), residues: 265 sheet: 0.29 (0.28), residues: 327 loop : -0.60 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 193 HIS 0.007 0.004 HIS R 102 PHE 0.002 0.000 PHE R 74 TYR 0.029 0.002 TYR R 344 ARG 0.000 0.000 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.11431 ( 419) hydrogen bonds : angle 5.85626 ( 1182) SS BOND : bond 0.00446 ( 4) SS BOND : angle 0.85865 ( 8) covalent geometry : bond 0.00310 ( 5935) covalent geometry : angle 0.66740 ( 8280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.640 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0686 time to fit residues: 4.4622 Evaluate side-chains 19 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 40.0000 chunk 78 optimal weight: 40.0000 chunk 43 optimal weight: 0.0000 chunk 26 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 50.0000 chunk 49 optimal weight: 40.0000 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 6.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027685 restraints weight = 103704.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 15)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027620 restraints weight = 105614.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027620 restraints weight = 107777.049| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 5939 Z= 0.238 Angle : 0.654 6.579 8288 Z= 0.380 Chirality : 0.042 0.167 1172 Planarity : 0.005 0.066 1111 Dihedral : 5.148 22.143 1048 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.28 % Allowed : 1.38 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: 0.57 (0.26), residues: 1031 helix: 2.03 (0.30), residues: 273 sheet: -0.45 (0.26), residues: 370 loop : 0.23 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 193 HIS 0.006 0.003 HIS R 300 PHE 0.017 0.001 PHE A 80 TYR 0.019 0.001 TYR A 321 ARG 0.003 0.002 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.04673 ( 419) hydrogen bonds : angle 6.41824 ( 1182) SS BOND : bond 0.00486 ( 4) SS BOND : angle 1.26385 ( 8) covalent geometry : bond 0.00393 ( 5935) covalent geometry : angle 0.65354 ( 8280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.652 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0608 time to fit residues: 3.2757 Evaluate side-chains 17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 0.2980 chunk 26 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 chunk 60 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.027024 restraints weight = 103073.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.027024 restraints weight = 103885.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.027024 restraints weight = 103885.729| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5939 Z= 0.146 Angle : 0.492 7.343 8288 Z= 0.269 Chirality : 0.040 0.153 1172 Planarity : 0.004 0.055 1111 Dihedral : 4.118 16.460 1048 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: 1.08 (0.27), residues: 1031 helix: 2.82 (0.31), residues: 274 sheet: -0.40 (0.28), residues: 346 loop : 0.43 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 193 HIS 0.006 0.002 HIS R 300 PHE 0.013 0.001 PHE A 80 TYR 0.012 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 419) hydrogen bonds : angle 5.13927 ( 1182) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.84841 ( 8) covalent geometry : bond 0.00243 ( 5935) covalent geometry : angle 0.49150 ( 8280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.631 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0596 time to fit residues: 2.8536 Evaluate side-chains 16 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 0.0000 chunk 99 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 overall best weight: 3.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026279 restraints weight = 105415.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026278 restraints weight = 106069.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026278 restraints weight = 106081.416| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5939 Z= 0.128 Angle : 0.471 7.353 8288 Z= 0.252 Chirality : 0.039 0.151 1172 Planarity : 0.004 0.052 1111 Dihedral : 3.811 15.038 1048 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: 1.31 (0.27), residues: 1031 helix: 3.15 (0.31), residues: 282 sheet: -0.26 (0.28), residues: 339 loop : 0.37 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP R 193 HIS 0.004 0.002 HIS R 300 PHE 0.007 0.001 PHE A 9 TYR 0.013 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 419) hydrogen bonds : angle 4.74826 ( 1182) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.55311 ( 8) covalent geometry : bond 0.00222 ( 5935) covalent geometry : angle 0.47081 ( 8280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 2.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1118 time to fit residues: 4.9559 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 99 optimal weight: 50.0000 chunk 2 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 67 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 38 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.035121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.023965 restraints weight = 109584.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.023965 restraints weight = 109219.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.023965 restraints weight = 109219.769| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5939 Z= 0.235 Angle : 0.611 7.105 8288 Z= 0.349 Chirality : 0.041 0.165 1172 Planarity : 0.005 0.048 1111 Dihedral : 5.243 22.821 1048 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: 0.31 (0.26), residues: 1031 helix: 2.68 (0.30), residues: 277 sheet: -1.00 (0.27), residues: 342 loop : -0.31 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.007 0.003 HIS R 300 PHE 0.015 0.001 PHE A 9 TYR 0.015 0.001 TYR R 144 ARG 0.004 0.002 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 419) hydrogen bonds : angle 6.36982 ( 1182) SS BOND : bond 0.01752 ( 4) SS BOND : angle 1.10481 ( 8) covalent geometry : bond 0.00396 ( 5935) covalent geometry : angle 0.61069 ( 8280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0583 time to fit residues: 2.7073 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 50.0000 chunk 88 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 1 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.032781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.022633 restraints weight = 115224.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.022688 restraints weight = 112389.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.022752 restraints weight = 109624.543| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.9314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5939 Z= 0.315 Angle : 0.734 7.693 8288 Z= 0.424 Chirality : 0.043 0.151 1172 Planarity : 0.006 0.054 1111 Dihedral : 6.667 27.179 1048 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1031 helix: 1.95 (0.30), residues: 270 sheet: -1.59 (0.28), residues: 305 loop : -1.17 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.009 0.004 HIS R 300 PHE 0.014 0.001 PHE A 9 TYR 0.020 0.001 TYR R 144 ARG 0.003 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 419) hydrogen bonds : angle 7.96041 ( 1182) SS BOND : bond 0.01189 ( 4) SS BOND : angle 1.24516 ( 8) covalent geometry : bond 0.00526 ( 5935) covalent geometry : angle 0.73307 ( 8280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.626 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0552 time to fit residues: 2.4548 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.022928 restraints weight = 112876.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.022995 restraints weight = 110030.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.022996 restraints weight = 107095.408| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 0.9196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5939 Z= 0.178 Angle : 0.560 7.682 8288 Z= 0.313 Chirality : 0.041 0.145 1172 Planarity : 0.005 0.050 1111 Dihedral : 5.491 23.386 1048 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -0.48 (0.26), residues: 1031 helix: 2.36 (0.30), residues: 276 sheet: -1.58 (0.27), residues: 325 loop : -0.98 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.004 0.002 HIS R 102 PHE 0.016 0.001 PHE A 9 TYR 0.017 0.001 TYR R 144 ARG 0.002 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 419) hydrogen bonds : angle 6.77209 ( 1182) SS BOND : bond 0.00447 ( 4) SS BOND : angle 1.09178 ( 8) covalent geometry : bond 0.00296 ( 5935) covalent geometry : angle 0.55973 ( 8280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.681 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0569 time to fit residues: 2.5757 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 43 optimal weight: 0.0970 chunk 91 optimal weight: 30.0000 chunk 47 optimal weight: 40.0000 overall best weight: 8.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.022578 restraints weight = 113384.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.022603 restraints weight = 110205.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.022660 restraints weight = 108908.481| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.9932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5939 Z= 0.238 Angle : 0.622 8.144 8288 Z= 0.351 Chirality : 0.041 0.141 1172 Planarity : 0.005 0.048 1111 Dihedral : 5.877 25.107 1048 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1031 helix: 2.39 (0.29), residues: 270 sheet: -1.76 (0.28), residues: 318 loop : -1.32 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.003 0.002 HIS R 102 PHE 0.014 0.001 PHE A 9 TYR 0.017 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 419) hydrogen bonds : angle 7.16486 ( 1182) SS BOND : bond 0.00771 ( 4) SS BOND : angle 1.41100 ( 8) covalent geometry : bond 0.00399 ( 5935) covalent geometry : angle 0.62052 ( 8280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0537 time to fit residues: 2.3086 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.022634 restraints weight = 113712.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.022672 restraints weight = 110513.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.022713 restraints weight = 108514.387| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5731 moved from start: 1.0168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5939 Z= 0.197 Angle : 0.563 8.273 8288 Z= 0.315 Chirality : 0.040 0.138 1172 Planarity : 0.005 0.048 1111 Dihedral : 5.428 24.233 1048 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -0.62 (0.27), residues: 1031 helix: 2.44 (0.30), residues: 278 sheet: -1.62 (0.30), residues: 307 loop : -1.32 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 193 HIS 0.004 0.002 HIS R 104 PHE 0.014 0.001 PHE A 9 TYR 0.017 0.001 TYR R 144 ARG 0.001 0.000 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 419) hydrogen bonds : angle 6.70342 ( 1182) SS BOND : bond 0.00543 ( 4) SS BOND : angle 0.92340 ( 8) covalent geometry : bond 0.00330 ( 5935) covalent geometry : angle 0.56283 ( 8280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.658 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0551 time to fit residues: 2.4726 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.022575 restraints weight = 116602.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.022663 restraints weight = 112135.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.022725 restraints weight = 108093.275| |-----------------------------------------------------------------------------| r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 1.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5939 Z= 0.247 Angle : 0.629 8.417 8288 Z= 0.358 Chirality : 0.041 0.144 1172 Planarity : 0.005 0.053 1111 Dihedral : 6.000 24.903 1048 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.60 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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: -1.02 (0.27), residues: 1031 helix: 2.28 (0.30), residues: 271 sheet: -1.91 (0.29), residues: 303 loop : -1.59 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 193 HIS 0.004 0.002 HIS R 104 PHE 0.015 0.001 PHE A 9 TYR 0.018 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 419) hydrogen bonds : angle 7.37949 ( 1182) SS BOND : bond 0.00733 ( 4) SS BOND : angle 1.18734 ( 8) covalent geometry : bond 0.00413 ( 5935) covalent geometry : angle 0.62811 ( 8280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.646 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0552 time to fit residues: 2.3904 Evaluate side-chains 14 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 64 optimal weight: 50.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.022982 restraints weight = 112718.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.023051 restraints weight = 109166.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.023113 restraints weight = 105932.184| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 1.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5939 Z= 0.146 Angle : 0.514 8.256 8288 Z= 0.284 Chirality : 0.040 0.138 1172 Planarity : 0.005 0.053 1111 Dihedral : 5.055 22.621 1048 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % 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 (0.27), residues: 1031 helix: 2.56 (0.30), residues: 285 sheet: -1.76 (0.31), residues: 283 loop : -1.39 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 193 HIS 0.004 0.001 HIS R 102 PHE 0.011 0.001 PHE A 9 TYR 0.015 0.001 TYR R 144 ARG 0.001 0.001 ARG R 372 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 419) hydrogen bonds : angle 6.38191 ( 1182) SS BOND : bond 0.00428 ( 4) SS BOND : angle 0.74002 ( 8) covalent geometry : bond 0.00247 ( 5935) covalent geometry : angle 0.51422 ( 8280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.20 seconds wall clock time: 34 minutes 57.87 seconds (2097.87 seconds total)