Starting phenix.real_space_refine on Tue Jul 29 16:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk9_25177/07_2025/7sk9_25177_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3711 2.51 5 N 918 2.21 5 O 1042 1.98 5 H 5561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11261 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4712 Chain: "F" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3280 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3213 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'CLR': 2, 'GJ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 291 " occ=0.50 ... (29 atoms not shown) pdb=" HE2BHIS A 291 " occ=0.50 Time building chain proxies: 7.49, per 1000 atoms: 0.67 Number of scatterers: 11261 At special positions: 0 Unit cell: (60.48, 64.8, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1042 8.00 N 918 7.00 C 3711 6.00 H 5561 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " 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: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 12 sheets defined 39.4% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 40 through 73 removed outlier: 4.211A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 106 removed outlier: 3.580A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.760A pdb=" N SER A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.851A pdb=" N THR A 152 " --> pdb=" O PHE A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 243 through 249 removed outlier: 4.065A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 280 removed outlier: 4.018A pdb=" N PHE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 305 removed outlier: 3.612A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.907A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.885A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.179A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.949A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.561A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA3, first strand: chain 'F' and resid 20 through 26 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.741A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 95 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.095A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.095A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.741A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 216 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR F 211 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 8 removed outlier: 4.070A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.796A pdb=" N GLU E 106 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 54 through 55 removed outlier: 5.969A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.637A pdb=" N ALA E 131 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.670A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS E 150 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 194 " --> pdb=" O LYS E 150 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5552 1.03 - 1.23: 29 1.23 - 1.42: 2489 1.42 - 1.62: 3314 1.62 - 1.82: 39 Bond restraints: 11423 Sorted by residual: bond pdb=" C14 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.416 1.492 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.495 1.558 -0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.457 1.517 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.446 1.505 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" C11 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.497 1.551 -0.054 2.00e-02 2.50e+03 7.32e+00 ... (remaining 11418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 20226 1.56 - 3.13: 272 3.13 - 4.69: 43 4.69 - 6.26: 8 6.26 - 7.82: 8 Bond angle restraints: 20557 Sorted by residual: angle pdb=" C22 CLR A 403 " pdb=" C23 CLR A 403 " pdb=" C24 CLR A 403 " ideal model delta sigma weight residual 111.95 104.13 7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 104.37 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C33 GJ9 A 401 " pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 112.14 119.71 -7.57 3.00e+00 1.11e-01 6.37e+00 angle pdb=" C08 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 108.48 116.01 -7.53 3.00e+00 1.11e-01 6.29e+00 angle pdb=" C06 GJ9 A 401 " pdb=" N05 GJ9 A 401 " pdb=" C37 GJ9 A 401 " ideal model delta sigma weight residual 121.17 114.07 7.10 3.00e+00 1.11e-01 5.61e+00 ... (remaining 20552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 5377 29.04 - 58.08: 206 58.08 - 87.12: 5 87.12 - 116.16: 6 116.16 - 145.19: 5 Dihedral angle restraints: 5599 sinusoidal: 3008 harmonic: 2591 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 178.86 -85.86 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" N10 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual -73.26 71.93 -145.19 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " pdb=" C14 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual 193.62 60.62 133.00 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 846 0.075 - 0.151: 67 0.151 - 0.226: 1 0.226 - 0.301: 2 0.301 - 0.376: 6 Chirality restraints: 922 Sorted by residual: chirality pdb=" C17 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C16 CLR A 403 " pdb=" C20 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" N10 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C34 GJ9 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.59 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.87 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 919 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 209 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C LEU A 209 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 209 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 225 " 0.011 2.00e-02 2.50e+03 6.79e-03 1.39e+00 pdb=" CG PHE A 225 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 225 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 225 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 225 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO F 166 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.015 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1428 2.25 - 2.84: 24621 2.84 - 3.42: 27440 3.42 - 4.01: 38245 4.01 - 4.60: 58028 Nonbonded interactions: 149762 Sorted by model distance: nonbonded pdb=" O GLN A 106 " pdb=" H GLN A 109 " model vdw 1.662 2.450 nonbonded pdb=" O HIS E 190 " pdb=" HE ARG E 212 " model vdw 1.706 2.450 nonbonded pdb=" O ASP E 83 " pdb=" HH TYR E 87 " model vdw 1.731 2.450 nonbonded pdb=" O THR A 147 " pdb=" HG SER F 57 " model vdw 1.744 2.450 nonbonded pdb=" H ILE F 32 " pdb=" OD1 ASN F 80 " model vdw 1.745 2.450 ... (remaining 149757 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 1.490 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: 0.200 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.360 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 5867 Z= 0.224 Angle : 0.620 7.825 8016 Z= 0.288 Chirality : 0.050 0.376 922 Planarity : 0.003 0.029 966 Dihedral : 15.645 145.195 2177 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.15 (0.35), residues: 707 helix: 2.71 (0.36), residues: 222 sheet: 0.15 (0.41), residues: 198 loop : -0.29 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 PHE 0.020 0.001 PHE A 225 TYR 0.018 0.001 TYR A 181 ARG 0.002 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.14656 ( 290) hydrogen bonds : angle 5.87488 ( 851) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.49826 ( 10) covalent geometry : bond 0.00469 ( 5862) covalent geometry : angle 0.62009 ( 8006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.836 Fit side-chains REVERT: E 25 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7382 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3109 time to fit residues: 37.5565 Evaluate side-chains 69 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094778 restraints weight = 40435.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.099504 restraints weight = 19075.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102586 restraints weight = 11482.702| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5867 Z= 0.142 Angle : 0.536 6.302 8016 Z= 0.276 Chirality : 0.040 0.143 922 Planarity : 0.003 0.033 966 Dihedral : 12.232 142.467 946 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.47 % Allowed : 6.30 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.04 (0.34), residues: 707 helix: 2.61 (0.34), residues: 233 sheet: 0.18 (0.40), residues: 203 loop : -0.57 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 PHE 0.016 0.001 PHE A 225 TYR 0.014 0.001 TYR A 181 ARG 0.001 0.000 ARG F 70 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 290) hydrogen bonds : angle 4.80560 ( 851) SS BOND : bond 0.00596 ( 5) SS BOND : angle 1.18958 ( 10) covalent geometry : bond 0.00321 ( 5862) covalent geometry : angle 0.53482 ( 8006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.816 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.3147 time to fit residues: 33.2105 Evaluate side-chains 71 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.116023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094540 restraints weight = 36866.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099050 restraints weight = 18018.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102053 restraints weight = 11086.801| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5867 Z= 0.157 Angle : 0.536 8.083 8016 Z= 0.274 Chirality : 0.040 0.142 922 Planarity : 0.003 0.034 966 Dihedral : 9.183 130.082 946 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.94 % Allowed : 7.56 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.96 (0.34), residues: 707 helix: 2.51 (0.34), residues: 237 sheet: 0.17 (0.40), residues: 203 loop : -0.68 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.017 0.001 PHE A 225 TYR 0.013 0.001 TYR F 162 ARG 0.001 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 290) hydrogen bonds : angle 4.66430 ( 851) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.55540 ( 10) covalent geometry : bond 0.00360 ( 5862) covalent geometry : angle 0.53309 ( 8006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.918 Fit side-chains REVERT: E 25 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7328 (ttm-80) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.3387 time to fit residues: 33.4126 Evaluate side-chains 73 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.116702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095506 restraints weight = 35931.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099960 restraints weight = 17566.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102924 restraints weight = 10831.234| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5867 Z= 0.125 Angle : 0.518 7.763 8016 Z= 0.261 Chirality : 0.039 0.177 922 Planarity : 0.003 0.033 966 Dihedral : 6.324 56.875 946 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.79 % Allowed : 8.19 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.04 (0.34), residues: 707 helix: 2.61 (0.34), residues: 237 sheet: 0.21 (0.39), residues: 203 loop : -0.66 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.017 0.001 PHE A 225 TYR 0.011 0.001 TYR F 162 ARG 0.001 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 290) hydrogen bonds : angle 4.48833 ( 851) SS BOND : bond 0.00407 ( 5) SS BOND : angle 1.14883 ( 10) covalent geometry : bond 0.00284 ( 5862) covalent geometry : angle 0.51626 ( 8006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.928 Fit side-chains REVERT: E 25 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7361 (ttm-80) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.3352 time to fit residues: 32.5485 Evaluate side-chains 71 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093912 restraints weight = 38915.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098519 restraints weight = 18643.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101580 restraints weight = 11368.111| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5867 Z= 0.149 Angle : 0.510 4.897 8016 Z= 0.265 Chirality : 0.039 0.139 922 Planarity : 0.003 0.035 966 Dihedral : 5.713 59.911 946 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.10 % Allowed : 8.98 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.96 (0.34), residues: 707 helix: 2.57 (0.34), residues: 237 sheet: 0.19 (0.39), residues: 203 loop : -0.76 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.020 0.001 PHE A 225 TYR 0.019 0.001 TYR A 181 ARG 0.001 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 290) hydrogen bonds : angle 4.46112 ( 851) SS BOND : bond 0.00456 ( 5) SS BOND : angle 1.03023 ( 10) covalent geometry : bond 0.00342 ( 5862) covalent geometry : angle 0.50867 ( 8006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.167 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 70 average time/residue: 0.4300 time to fit residues: 41.9139 Evaluate side-chains 72 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 35 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 24 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.1954 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.118972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097289 restraints weight = 38824.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101988 restraints weight = 18200.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105092 restraints weight = 10968.315| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5867 Z= 0.088 Angle : 0.470 4.753 8016 Z= 0.240 Chirality : 0.039 0.131 922 Planarity : 0.003 0.031 966 Dihedral : 4.972 53.893 946 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.94 % Allowed : 9.29 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.30 (0.35), residues: 707 helix: 2.88 (0.34), residues: 237 sheet: 0.34 (0.40), residues: 203 loop : -0.56 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.002 0.001 HIS A 298 PHE 0.017 0.001 PHE A 225 TYR 0.016 0.001 TYR A 181 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 290) hydrogen bonds : angle 4.23244 ( 851) SS BOND : bond 0.00276 ( 5) SS BOND : angle 0.71969 ( 10) covalent geometry : bond 0.00195 ( 5862) covalent geometry : angle 0.46959 ( 8006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.998 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.3306 time to fit residues: 36.5180 Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095076 restraints weight = 38715.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099672 restraints weight = 18490.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102742 restraints weight = 11278.352| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5867 Z= 0.137 Angle : 0.494 4.606 8016 Z= 0.256 Chirality : 0.039 0.137 922 Planarity : 0.003 0.034 966 Dihedral : 5.142 58.599 946 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.10 % Allowed : 10.08 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.19 (0.35), residues: 707 helix: 2.79 (0.34), residues: 237 sheet: 0.28 (0.39), residues: 203 loop : -0.64 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.019 0.001 PHE A 225 TYR 0.013 0.001 TYR A 181 ARG 0.003 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 290) hydrogen bonds : angle 4.28222 ( 851) SS BOND : bond 0.00437 ( 5) SS BOND : angle 0.90182 ( 10) covalent geometry : bond 0.00317 ( 5862) covalent geometry : angle 0.49374 ( 8006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.841 Fit side-chains REVERT: E 25 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7415 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.3185 time to fit residues: 32.1789 Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093820 restraints weight = 40429.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098576 restraints weight = 19086.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101658 restraints weight = 11412.781| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5867 Z= 0.147 Angle : 0.509 4.519 8016 Z= 0.264 Chirality : 0.039 0.138 922 Planarity : 0.003 0.035 966 Dihedral : 5.277 61.787 946 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.26 % Allowed : 10.39 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.06 (0.34), residues: 707 helix: 2.70 (0.34), residues: 237 sheet: 0.20 (0.39), residues: 203 loop : -0.72 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.020 0.001 PHE A 225 TYR 0.013 0.001 TYR F 162 ARG 0.002 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 290) hydrogen bonds : angle 4.32550 ( 851) SS BOND : bond 0.00454 ( 5) SS BOND : angle 0.88593 ( 10) covalent geometry : bond 0.00337 ( 5862) covalent geometry : angle 0.50797 ( 8006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.846 Fit side-chains REVERT: E 25 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7291 (ttm-80) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.3227 time to fit residues: 31.8034 Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 208 TRP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095095 restraints weight = 34691.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099483 restraints weight = 17259.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.102375 restraints weight = 10739.962| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5867 Z= 0.131 Angle : 0.497 4.527 8016 Z= 0.257 Chirality : 0.039 0.139 922 Planarity : 0.003 0.034 966 Dihedral : 5.210 60.486 946 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.10 % Allowed : 10.71 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.12 (0.34), residues: 707 helix: 2.74 (0.34), residues: 237 sheet: 0.23 (0.39), residues: 203 loop : -0.66 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.019 0.001 PHE A 225 TYR 0.010 0.001 TYR F 162 ARG 0.001 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 290) hydrogen bonds : angle 4.28346 ( 851) SS BOND : bond 0.00420 ( 5) SS BOND : angle 0.80041 ( 10) covalent geometry : bond 0.00300 ( 5862) covalent geometry : angle 0.49637 ( 8006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.866 Fit side-chains REVERT: E 25 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7342 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.3231 time to fit residues: 32.3070 Evaluate side-chains 75 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 39 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.116705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095116 restraints weight = 37938.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099699 restraints weight = 18157.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102757 restraints weight = 11063.924| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5867 Z= 0.116 Angle : 0.489 4.533 8016 Z= 0.252 Chirality : 0.039 0.137 922 Planarity : 0.003 0.034 966 Dihedral : 5.107 58.645 946 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.10 % Allowed : 10.55 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.18 (0.34), residues: 707 helix: 2.79 (0.34), residues: 237 sheet: 0.24 (0.39), residues: 203 loop : -0.62 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.019 0.001 PHE A 225 TYR 0.015 0.001 TYR A 181 ARG 0.001 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 290) hydrogen bonds : angle 4.24094 ( 851) SS BOND : bond 0.00391 ( 5) SS BOND : angle 0.74080 ( 10) covalent geometry : bond 0.00264 ( 5862) covalent geometry : angle 0.48887 ( 8006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.888 Fit side-chains REVERT: E 25 ARG cc_start: 0.7652 (mtp85) cc_final: 0.7335 (ttm-80) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.3162 time to fit residues: 31.6839 Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 33 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.0270 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097248 restraints weight = 38328.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101902 restraints weight = 18123.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104977 restraints weight = 10948.812| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5867 Z= 0.091 Angle : 0.472 4.638 8016 Z= 0.241 Chirality : 0.039 0.132 922 Planarity : 0.003 0.032 966 Dihedral : 4.850 52.648 946 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.10 % Allowed : 10.55 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.42 (0.35), residues: 707 helix: 2.98 (0.34), residues: 237 sheet: 0.36 (0.39), residues: 202 loop : -0.44 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 PHE 0.018 0.001 PHE A 225 TYR 0.014 0.001 TYR A 181 ARG 0.001 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 290) hydrogen bonds : angle 4.12119 ( 851) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.63510 ( 10) covalent geometry : bond 0.00206 ( 5862) covalent geometry : angle 0.47130 ( 8006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4199.61 seconds wall clock time: 73 minutes 55.46 seconds (4435.46 seconds total)