Starting phenix.real_space_refine on Sat Apr 6 05:55:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wu1_37849/04_2024/8wu1_37849_updated.pdb" } resolution = 3.2 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= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 31 5.16 5 C 4648 2.51 5 N 1226 2.21 5 O 1338 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2577 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 330} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 176 Chain: "H" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1314 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 184} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "L" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1191 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2139 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 3 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TPO:plan-1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Classifications: {'peptide': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.62 Number of scatterers: 7250 At special positions: 0 Unit cell: (151.59, 102.3, 88.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 6 15.00 F 1 9.00 O 1338 8.00 N 1226 7.00 C 4648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 14 sheets defined 23.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'L' and resid 184 through 186 No H-bonds generated for 'chain 'L' and resid 184 through 186' Processing helix chain 'R' and resid 113 through 140 removed outlier: 4.100A pdb=" N LEU R 117 " --> pdb=" O PRO R 113 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 149 No H-bonds generated for 'chain 'R' and resid 146 through 149' Processing helix chain 'R' and resid 151 through 178 Processing helix chain 'R' and resid 188 through 219 Processing helix chain 'R' and resid 223 through 226 No H-bonds generated for 'chain 'R' and resid 223 through 226' Processing helix chain 'R' and resid 230 through 252 Proline residue: R 251 - end of helix Processing helix chain 'R' and resid 274 through 308 Processing helix chain 'R' and resid 341 through 368 Proline residue: R 358 - end of helix removed outlier: 3.556A pdb=" N ALA R 361 " --> pdb=" O GLY R 357 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 398 Proline residue: R 394 - end of helix Processing helix chain 'R' and resid 402 through 407 Processing sheet with id= A, first strand: chain 'C' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.570A pdb=" N GLU C 169 " --> pdb=" O PHE C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.979A pdb=" N VAL C 55 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 57 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 83 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N CYS C 59 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 81 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.769A pdb=" N SER C 202 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 207 through 209 removed outlier: 6.104A pdb=" N THR C 350 " --> pdb=" O TYR C 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 342 through 349 removed outlier: 3.527A pdb=" N PHE C 349 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 8 through 10 Processing sheet with id= H, first strand: chain 'H' and resid 117 through 119 removed outlier: 6.033A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.878A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.509A pdb=" N LYS H 219 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.680A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= M, first strand: chain 'L' and resid 12 through 14 removed outlier: 3.705A pdb=" N ALA L 14 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.536A pdb=" N THR L 181 " --> pdb=" O ASN L 159 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN L 159 " --> pdb=" O THR L 181 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 927 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: 2.16 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1123 1.31 - 1.43: 1950 1.43 - 1.56: 4269 1.56 - 1.68: 26 1.68 - 1.81: 39 Bond restraints: 7407 Sorted by residual: bond pdb=" CAX KCA R 501 " pdb=" CBC KCA R 501 " ideal model delta sigma weight residual 1.399 1.577 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" CAY KCA R 501 " pdb=" CAZ KCA R 501 " ideal model delta sigma weight residual 1.402 1.579 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" CAV KCA R 501 " pdb=" CAW KCA R 501 " ideal model delta sigma weight residual 1.385 1.545 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" CAS KCA R 501 " pdb=" CAT KCA R 501 " ideal model delta sigma weight residual 1.380 1.534 -0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" CAR KCA R 501 " pdb=" CAS KCA R 501 " ideal model delta sigma weight residual 1.389 1.542 -0.153 2.00e-02 2.50e+03 5.85e+01 ... (remaining 7402 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.15: 257 107.15 - 113.88: 4330 113.88 - 120.60: 2735 120.60 - 127.33: 2747 127.33 - 134.06: 88 Bond angle restraints: 10157 Sorted by residual: angle pdb=" CB TPO R 432 " pdb=" OG1 TPO R 432 " pdb=" P TPO R 432 " ideal model delta sigma weight residual 119.31 107.40 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB TPO R 431 " pdb=" OG1 TPO R 431 " pdb=" P TPO R 431 " ideal model delta sigma weight residual 119.31 108.34 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C TYR L 141 " pdb=" N PRO L 142 " pdb=" CD PRO L 142 " ideal model delta sigma weight residual 120.60 112.66 7.94 2.20e+00 2.07e-01 1.30e+01 angle pdb=" OG1 TPO R 431 " pdb=" P TPO R 431 " pdb=" O1P TPO R 431 " ideal model delta sigma weight residual 100.43 109.61 -9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" OG1 TPO R 432 " pdb=" P TPO R 432 " pdb=" O1P TPO R 432 " ideal model delta sigma weight residual 100.43 109.58 -9.15 3.00e+00 1.11e-01 9.29e+00 ... (remaining 10152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4014 15.82 - 31.63: 279 31.63 - 47.44: 62 47.44 - 63.26: 13 63.26 - 79.07: 2 Dihedral angle restraints: 4370 sinusoidal: 1406 harmonic: 2964 Sorted by residual: dihedral pdb=" CB CYS R 257 " pdb=" SG CYS R 257 " pdb=" SG CYS R 264 " pdb=" CB CYS R 264 " ideal model delta sinusoidal sigma weight residual -86.00 -117.12 31.12 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CA PHE R 268 " pdb=" C PHE R 268 " pdb=" N PRO R 269 " pdb=" CA PRO R 269 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASP C 260 " pdb=" CB ASP C 260 " pdb=" CG ASP C 260 " pdb=" OD1 ASP C 260 " ideal model delta sinusoidal sigma weight residual -30.00 -81.28 51.28 1 2.00e+01 2.50e-03 8.99e+00 ... (remaining 4367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 918 0.040 - 0.080: 220 0.080 - 0.121: 87 0.121 - 0.161: 16 0.161 - 0.201: 1 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CB THR R 344 " pdb=" CA THR R 344 " pdb=" OG1 THR R 344 " pdb=" CG2 THR R 344 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA KCA R 501 " pdb=" N KCA R 501 " pdb=" C KCA R 501 " pdb=" CB KCA R 501 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1239 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 141 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO L 142 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO L 142 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO L 142 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 350 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C VAL R 350 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 350 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL R 351 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 80 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO L 81 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 81 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 81 " -0.026 5.00e-02 4.00e+02 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 835 2.75 - 3.28: 7095 3.28 - 3.82: 11442 3.82 - 4.36: 12758 4.36 - 4.90: 22910 Nonbonded interactions: 55040 Sorted by model distance: nonbonded pdb=" NZ LYS L 40 " pdb=" O GLU L 82 " model vdw 2.208 2.520 nonbonded pdb=" OD1 ASP R 272 " pdb=" N GLU R 273 " model vdw 2.226 2.520 nonbonded pdb=" NE2 GLN C 130 " pdb=" O ARG C 282 " model vdw 2.243 2.520 nonbonded pdb=" OD1 ASP C 240 " pdb=" NE2 GLN C 248 " model vdw 2.259 2.520 nonbonded pdb=" OG SER R 265 " pdb=" O PHE R 268 " model vdw 2.267 2.440 ... (remaining 55035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.710 Find NCS groups from input model: 0.200 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.008 0.178 7407 Z= 0.550 Angle : 0.621 11.908 10157 Z= 0.306 Chirality : 0.043 0.201 1242 Planarity : 0.005 0.107 1266 Dihedral : 11.916 79.075 2439 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 981 helix: 0.96 (0.33), residues: 248 sheet: -0.60 (0.28), residues: 318 loop : -0.93 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 279 HIS 0.010 0.001 HIS C 353 PHE 0.016 0.001 PHE H 105 TYR 0.015 0.001 TYR H 107 ARG 0.008 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.702 Fit side-chains REVERT: C 160 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7331 (tppt) REVERT: R 214 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6929 (mpt180) REVERT: R 400 ARG cc_start: 0.7038 (mmm160) cc_final: 0.6135 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2227 time to fit residues: 39.1305 Evaluate side-chains 119 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7407 Z= 0.224 Angle : 0.541 8.951 10157 Z= 0.275 Chirality : 0.042 0.153 1242 Planarity : 0.004 0.071 1266 Dihedral : 5.583 66.243 1104 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.59 % Allowed : 7.06 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.40 (0.27), residues: 981 helix: 0.85 (0.33), residues: 247 sheet: -0.45 (0.29), residues: 318 loop : -0.66 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 279 HIS 0.007 0.001 HIS R 178 PHE 0.020 0.002 PHE H 105 TYR 0.020 0.001 TYR H 107 ARG 0.006 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.669 Fit side-chains REVERT: C 160 LYS cc_start: 0.8287 (tmmt) cc_final: 0.7543 (tppt) REVERT: R 129 PHE cc_start: 0.7008 (t80) cc_final: 0.6787 (t80) REVERT: R 400 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6154 (tmt-80) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.1910 time to fit residues: 33.8628 Evaluate side-chains 126 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 302 HIS Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7407 Z= 0.338 Angle : 0.575 8.760 10157 Z= 0.296 Chirality : 0.043 0.163 1242 Planarity : 0.004 0.057 1266 Dihedral : 5.750 62.241 1104 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.74 % Allowed : 10.95 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.45 (0.27), residues: 981 helix: 0.70 (0.33), residues: 247 sheet: -0.45 (0.29), residues: 326 loop : -0.64 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 279 HIS 0.007 0.001 HIS C 353 PHE 0.029 0.002 PHE H 105 TYR 0.021 0.001 TYR H 107 ARG 0.006 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.786 Fit side-chains REVERT: C 160 LYS cc_start: 0.8376 (tmmt) cc_final: 0.7696 (tppt) REVERT: L 31 SER cc_start: 0.8646 (p) cc_final: 0.8382 (p) REVERT: R 400 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6166 (tmt-80) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.2138 time to fit residues: 37.0774 Evaluate side-chains 132 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 overall best weight: 0.6816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7407 Z= 0.177 Angle : 0.526 11.525 10157 Z= 0.263 Chirality : 0.042 0.158 1242 Planarity : 0.004 0.058 1266 Dihedral : 5.417 62.080 1104 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.88 % Allowed : 12.25 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 981 helix: 0.92 (0.34), residues: 242 sheet: -0.21 (0.29), residues: 314 loop : -0.54 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 279 HIS 0.003 0.001 HIS C 353 PHE 0.017 0.001 PHE H 105 TYR 0.016 0.001 TYR H 107 ARG 0.006 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.812 Fit side-chains REVERT: C 160 LYS cc_start: 0.8252 (tmmt) cc_final: 0.7511 (tppt) REVERT: R 209 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8816 (mm) REVERT: R 247 ILE cc_start: 0.8088 (mm) cc_final: 0.7807 (mt) REVERT: R 400 ARG cc_start: 0.7113 (mmm160) cc_final: 0.6219 (tmt-80) outliers start: 20 outliers final: 12 residues processed: 134 average time/residue: 0.1985 time to fit residues: 35.5161 Evaluate side-chains 131 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7407 Z= 0.204 Angle : 0.530 9.353 10157 Z= 0.266 Chirality : 0.041 0.153 1242 Planarity : 0.004 0.059 1266 Dihedral : 5.336 60.384 1104 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.31 % Allowed : 13.83 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.10 (0.27), residues: 981 helix: 0.93 (0.34), residues: 242 sheet: -0.13 (0.30), residues: 316 loop : -0.48 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 106 HIS 0.004 0.001 HIS C 353 PHE 0.019 0.001 PHE H 105 TYR 0.017 0.001 TYR H 107 ARG 0.008 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.811 Fit side-chains REVERT: C 160 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7602 (tppt) REVERT: R 209 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8855 (mm) REVERT: R 247 ILE cc_start: 0.8041 (mm) cc_final: 0.7677 (mt) REVERT: R 400 ARG cc_start: 0.7164 (mmm160) cc_final: 0.6251 (tmt-80) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.2052 time to fit residues: 35.0770 Evaluate side-chains 134 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7407 Z= 0.368 Angle : 0.590 9.396 10157 Z= 0.303 Chirality : 0.044 0.174 1242 Planarity : 0.004 0.064 1266 Dihedral : 5.756 65.382 1104 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.25 (0.27), residues: 981 helix: 0.74 (0.33), residues: 240 sheet: -0.27 (0.29), residues: 326 loop : -0.47 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 106 HIS 0.007 0.001 HIS C 353 PHE 0.032 0.002 PHE H 105 TYR 0.021 0.002 TYR H 107 ARG 0.009 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.764 Fit side-chains REVERT: C 160 LYS cc_start: 0.8357 (tmmt) cc_final: 0.7787 (tppt) REVERT: R 209 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8908 (mm) REVERT: R 400 ARG cc_start: 0.7357 (mmm160) cc_final: 0.6453 (tmt-80) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2055 time to fit residues: 35.6027 Evaluate side-chains 132 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7407 Z= 0.191 Angle : 0.531 9.631 10157 Z= 0.269 Chirality : 0.041 0.157 1242 Planarity : 0.004 0.064 1266 Dihedral : 5.424 65.161 1104 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.16 % Allowed : 16.57 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.05 (0.27), residues: 981 helix: 0.91 (0.34), residues: 242 sheet: -0.09 (0.29), residues: 318 loop : -0.42 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 279 HIS 0.003 0.000 HIS C 353 PHE 0.017 0.001 PHE H 105 TYR 0.017 0.001 TYR H 107 ARG 0.009 0.000 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 0.740 Fit side-chains REVERT: C 160 LYS cc_start: 0.8270 (tmmt) cc_final: 0.7717 (tppt) REVERT: R 209 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8901 (mm) REVERT: R 400 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6363 (tmt-80) outliers start: 15 outliers final: 14 residues processed: 129 average time/residue: 0.2000 time to fit residues: 34.1916 Evaluate side-chains 132 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.0970 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7407 Z= 0.477 Angle : 0.633 9.584 10157 Z= 0.329 Chirality : 0.045 0.162 1242 Planarity : 0.004 0.069 1266 Dihedral : 5.963 71.171 1104 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.88 % Allowed : 16.86 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.33 (0.27), residues: 981 helix: 0.70 (0.33), residues: 238 sheet: -0.26 (0.29), residues: 321 loop : -0.59 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 279 HIS 0.008 0.001 HIS C 353 PHE 0.038 0.002 PHE H 105 TYR 0.021 0.002 TYR H 107 ARG 0.009 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7664 (ptp90) cc_final: 0.7318 (ptp90) REVERT: L 31 SER cc_start: 0.8577 (p) cc_final: 0.8316 (p) REVERT: R 209 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8935 (mm) REVERT: R 400 ARG cc_start: 0.7424 (mmm160) cc_final: 0.6629 (tmt-80) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.2148 time to fit residues: 38.2775 Evaluate side-chains 141 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 303 SER Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 353 ILE Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7407 Z= 0.181 Angle : 0.556 9.568 10157 Z= 0.280 Chirality : 0.042 0.153 1242 Planarity : 0.004 0.070 1266 Dihedral : 5.534 70.169 1104 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.87 % Allowed : 18.44 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.10 (0.27), residues: 981 helix: 0.87 (0.34), residues: 242 sheet: -0.11 (0.29), residues: 318 loop : -0.45 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 279 HIS 0.003 0.001 HIS C 111 PHE 0.021 0.001 PHE R 177 TYR 0.018 0.001 TYR H 107 ARG 0.009 0.001 ARG R 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7389 (ptp90) REVERT: R 209 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8919 (mm) REVERT: R 400 ARG cc_start: 0.7410 (mmm160) cc_final: 0.6548 (tmt-80) outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.1969 time to fit residues: 33.4112 Evaluate side-chains 128 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 79 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7407 Z= 0.204 Angle : 0.935 59.195 10157 Z= 0.542 Chirality : 0.043 0.368 1242 Planarity : 0.004 0.073 1266 Dihedral : 5.530 70.188 1104 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.87 % Allowed : 19.16 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.10 (0.27), residues: 981 helix: 0.87 (0.34), residues: 242 sheet: -0.11 (0.29), residues: 318 loop : -0.45 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 279 HIS 0.004 0.001 HIS C 111 PHE 0.021 0.001 PHE R 177 TYR 0.018 0.001 TYR H 107 ARG 0.008 0.001 ARG R 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: C 161 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7394 (ptp90) REVERT: R 209 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8919 (mm) REVERT: R 400 ARG cc_start: 0.7411 (mmm160) cc_final: 0.6548 (tmt-80) outliers start: 13 outliers final: 12 residues processed: 126 average time/residue: 0.1908 time to fit residues: 32.2450 Evaluate side-chains 130 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 187 ASN Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.174637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113976 restraints weight = 9792.683| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.02 r_work: 0.3221 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 7407 Z= 0.315 Angle : 0.908 47.630 10157 Z= 0.635 Chirality : 0.042 0.256 1242 Planarity : 0.005 0.091 1266 Dihedral : 5.530 70.188 1104 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.87 % Allowed : 19.16 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.32 % 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: -0.10 (0.27), residues: 981 helix: 0.87 (0.34), residues: 242 sheet: -0.11 (0.29), residues: 318 loop : -0.45 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 279 HIS 0.004 0.001 HIS C 111 PHE 0.021 0.001 PHE R 177 TYR 0.018 0.001 TYR H 107 ARG 0.008 0.001 ARG R 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.12 seconds wall clock time: 34 minutes 43.58 seconds (2083.58 seconds total)