Starting phenix.real_space_refine on Mon Mar 11 02:36:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tlm_41370/03_2024/8tlm_41370.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1267 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 3510 2.51 5 N 860 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1606 Classifications: {'peptide': 215} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 206} Chain: "C" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2166 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 5, 'TRANS': 260} Chain breaks: 2 Time building chain proxies: 3.38, per 1000 atoms: 0.63 Number of scatterers: 5400 At special positions: 0 Unit cell: (65.96, 62.08, 148.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1005 8.00 N 860 7.00 C 3510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 183 " 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 10 sheets defined 38.4% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.149A pdb=" N THR A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.848A pdb=" N GLY A 199 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.035A pdb=" N ALA B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 186 through 191 removed outlier: 4.066A pdb=" N GLU B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 186 through 191' Processing helix chain 'C' and resid 34 through 63 Processing helix chain 'C' and resid 68 through 96 removed outlier: 3.989A pdb=" N VAL C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 101 through 137 removed outlier: 4.390A pdb=" N MET C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 110 " --> pdb=" O CYS C 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.911A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LYS C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 170 Proline residue: C 167 - end of helix removed outlier: 3.837A pdb=" N VAL C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 207 removed outlier: 4.079A pdb=" N LYS C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 226 removed outlier: 3.562A pdb=" N ILE C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 220 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 265 removed outlier: 3.832A pdb=" N TRP C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 274 through 304 removed outlier: 3.707A pdb=" N ILE C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS C 292 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N CYS C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 304 through 312 removed outlier: 3.568A pdb=" N LYS C 308 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 310 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.916A pdb=" N ALA A 33 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.016A pdb=" N TYR A 185 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.016A pdb=" N TYR A 185 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 4.789A pdb=" N TYR A 203 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 12.108A pdb=" N CYS B 23 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N THR B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N GLN B 27 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.283A pdb=" N VAL B 11 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 117 through 121 removed outlier: 5.895A pdb=" N TYR B 176 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 301 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1633 1.34 - 1.46: 1443 1.46 - 1.58: 2421 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 5531 Sorted by residual: bond pdb=" N ASN C 33 " pdb=" CA ASN C 33 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ALA B 1 " pdb=" CA ALA B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLN A 2 " pdb=" CA GLN A 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" CA VAL C 252 " pdb=" CB VAL C 252 " ideal model delta sigma weight residual 1.534 1.540 -0.006 6.80e-03 2.16e+04 7.53e-01 bond pdb=" N GLY C 150 " pdb=" CA GLY C 150 " ideal model delta sigma weight residual 1.454 1.446 0.008 1.24e-02 6.50e+03 3.93e-01 ... (remaining 5526 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.40: 175 107.40 - 114.05: 3197 114.05 - 120.70: 2203 120.70 - 127.34: 1899 127.34 - 133.99: 62 Bond angle restraints: 7536 Sorted by residual: angle pdb=" C VAL C 295 " pdb=" CA VAL C 295 " pdb=" CB VAL C 295 " ideal model delta sigma weight residual 112.16 108.97 3.19 1.63e+00 3.76e-01 3.84e+00 angle pdb=" CA CYS B 137 " pdb=" CB CYS B 137 " pdb=" SG CYS B 137 " ideal model delta sigma weight residual 114.40 118.38 -3.98 2.30e+00 1.89e-01 2.99e+00 angle pdb=" C LYS A 152 " pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta sigma weight residual 122.82 125.18 -2.36 1.42e+00 4.96e-01 2.77e+00 angle pdb=" C VAL C 100 " pdb=" CA VAL C 100 " pdb=" CB VAL C 100 " ideal model delta sigma weight residual 111.65 109.62 2.03 1.22e+00 6.72e-01 2.77e+00 angle pdb=" N TYR A 107 " pdb=" CA TYR A 107 " pdb=" C TYR A 107 " ideal model delta sigma weight residual 112.04 114.39 -2.35 1.44e+00 4.82e-01 2.66e+00 ... (remaining 7531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 3012 16.86 - 33.71: 181 33.71 - 50.57: 38 50.57 - 67.43: 10 67.43 - 84.28: 1 Dihedral angle restraints: 3242 sinusoidal: 1210 harmonic: 2032 Sorted by residual: dihedral pdb=" CB CYS B 137 " pdb=" SG CYS B 137 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 48.40 44.60 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS A 149 " pdb=" SG CYS A 149 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 61.13 31.87 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA THR A 106 " pdb=" C THR A 106 " pdb=" N TYR A 107 " pdb=" CA TYR A 107 " ideal model delta harmonic sigma weight residual 180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 574 0.031 - 0.061: 215 0.061 - 0.091: 52 0.091 - 0.122: 46 0.122 - 0.152: 6 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 890 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 157 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 158 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 59 " -0.004 2.00e-02 2.50e+03 8.67e-03 7.52e-01 pdb=" C VAL C 59 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL C 59 " -0.006 2.00e-02 2.50e+03 pdb=" N LEU C 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 219 " 0.004 2.00e-02 2.50e+03 8.23e-03 6.77e-01 pdb=" C ILE C 219 " -0.014 2.00e-02 2.50e+03 pdb=" O ILE C 219 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS C 220 " 0.005 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 40 2.63 - 3.19: 4898 3.19 - 3.76: 7695 3.76 - 4.33: 11189 4.33 - 4.90: 19177 Nonbonded interactions: 42999 Sorted by model distance: nonbonded pdb=" OD2 ASP A 101 " pdb=" OG1 THR C 103 " model vdw 2.057 2.440 nonbonded pdb=" OG SER C 128 " pdb=" OH TYR C 218 " model vdw 2.063 2.440 nonbonded pdb=" O PHE C 122 " pdb=" OG1 THR C 125 " model vdw 2.258 2.440 nonbonded pdb=" OG SER A 212 " pdb=" OG1 THR A 214 " model vdw 2.330 2.440 nonbonded pdb=" NZ LYS C 107 " pdb=" O TYR C 172 " model vdw 2.386 2.520 ... (remaining 42994 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 4.870 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5531 Z= 0.177 Angle : 0.494 6.558 7536 Z= 0.274 Chirality : 0.040 0.152 893 Planarity : 0.003 0.040 921 Dihedral : 11.712 84.285 1921 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.36 (0.33), residues: 684 helix: 1.86 (0.35), residues: 214 sheet: 1.47 (0.37), residues: 191 loop : -0.24 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS B 192 PHE 0.009 0.001 PHE C 84 TYR 0.008 0.001 TYR C 184 ARG 0.001 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.586 Fit side-chains REVERT: A 153 ASP cc_start: 0.7747 (p0) cc_final: 0.7468 (p0) REVERT: B 45 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6956 (mm-30) REVERT: B 127 GLN cc_start: 0.8678 (tt0) cc_final: 0.8285 (tt0) REVERT: B 150 GLN cc_start: 0.7421 (mt0) cc_final: 0.6949 (mt0) REVERT: B 214 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7334 (mtm-85) REVERT: C 195 LYS cc_start: 0.8216 (tttp) cc_final: 0.7989 (tttp) REVERT: C 216 PHE cc_start: 0.7519 (t80) cc_final: 0.7270 (t80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.1358 time to fit residues: 126.8860 Evaluate side-chains 87 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5531 Z= 0.285 Angle : 0.593 6.754 7536 Z= 0.309 Chirality : 0.043 0.167 893 Planarity : 0.004 0.042 921 Dihedral : 4.515 18.633 742 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.64 % Allowed : 10.34 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.32), residues: 684 helix: 1.62 (0.34), residues: 215 sheet: 1.52 (0.36), residues: 196 loop : -0.42 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.002 0.001 HIS B 192 PHE 0.021 0.002 PHE C 254 TYR 0.014 0.002 TYR C 132 ARG 0.004 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.627 Fit side-chains REVERT: B 150 GLN cc_start: 0.7413 (mt0) cc_final: 0.6981 (mt0) REVERT: B 214 ARG cc_start: 0.7531 (mtp85) cc_final: 0.7177 (mtm-85) REVERT: C 133 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7143 (tt) REVERT: C 195 LYS cc_start: 0.8260 (tttp) cc_final: 0.8016 (tttp) REVERT: C 204 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7308 (mp) REVERT: C 216 PHE cc_start: 0.7605 (t80) cc_final: 0.7374 (t80) REVERT: C 283 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (t70) outliers start: 10 outliers final: 3 residues processed: 90 average time/residue: 1.1149 time to fit residues: 105.2141 Evaluate side-chains 86 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5531 Z= 0.215 Angle : 0.544 6.755 7536 Z= 0.285 Chirality : 0.042 0.180 893 Planarity : 0.003 0.042 921 Dihedral : 4.438 18.515 742 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 13.79 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.20 (0.32), residues: 684 helix: 1.62 (0.34), residues: 216 sheet: 1.69 (0.37), residues: 195 loop : -0.55 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS C 292 PHE 0.018 0.001 PHE C 214 TYR 0.010 0.001 TYR C 218 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.690 Fit side-chains REVERT: B 150 GLN cc_start: 0.7368 (mt0) cc_final: 0.6920 (mt0) REVERT: B 214 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7234 (mtm-85) REVERT: C 133 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7204 (tt) REVERT: C 195 LYS cc_start: 0.8151 (tttp) cc_final: 0.7920 (tttp) REVERT: C 216 PHE cc_start: 0.7447 (t80) cc_final: 0.7164 (t80) REVERT: C 283 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (t70) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 1.1305 time to fit residues: 107.7046 Evaluate side-chains 88 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5531 Z= 0.446 Angle : 0.647 7.011 7536 Z= 0.339 Chirality : 0.046 0.207 893 Planarity : 0.004 0.044 921 Dihedral : 4.903 20.780 742 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.94 % Allowed : 14.45 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.87 (0.32), residues: 684 helix: 1.33 (0.34), residues: 214 sheet: 1.61 (0.37), residues: 194 loop : -0.80 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 47 HIS 0.003 0.001 HIS B 192 PHE 0.018 0.002 PHE C 290 TYR 0.015 0.002 TYR C 218 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.653 Fit side-chains REVERT: A 153 ASP cc_start: 0.8360 (p0) cc_final: 0.8058 (p0) REVERT: B 106 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 150 GLN cc_start: 0.7532 (mt0) cc_final: 0.7134 (mt0) REVERT: C 133 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7325 (tt) REVERT: C 211 PHE cc_start: 0.7613 (t80) cc_final: 0.7258 (t80) REVERT: C 216 PHE cc_start: 0.7492 (t80) cc_final: 0.7275 (t80) REVERT: C 283 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7707 (t70) outliers start: 24 outliers final: 10 residues processed: 96 average time/residue: 1.0259 time to fit residues: 103.4261 Evaluate side-chains 98 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.0070 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5531 Z= 0.192 Angle : 0.538 7.514 7536 Z= 0.281 Chirality : 0.041 0.175 893 Planarity : 0.003 0.041 921 Dihedral : 4.472 19.788 742 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.96 % Allowed : 17.08 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.32), residues: 684 helix: 1.58 (0.34), residues: 216 sheet: 1.61 (0.37), residues: 195 loop : -0.74 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS B 201 PHE 0.015 0.001 PHE C 290 TYR 0.016 0.001 TYR C 132 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8206 (t0) REVERT: B 150 GLN cc_start: 0.7374 (mt0) cc_final: 0.6942 (mt0) REVERT: C 133 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 211 PHE cc_start: 0.7436 (t80) cc_final: 0.7097 (t80) REVERT: C 283 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7552 (t70) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 1.0798 time to fit residues: 112.1696 Evaluate side-chains 95 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5531 Z= 0.285 Angle : 0.573 7.728 7536 Z= 0.300 Chirality : 0.043 0.178 893 Planarity : 0.004 0.044 921 Dihedral : 4.558 19.935 742 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.11 % Allowed : 17.73 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.98 (0.32), residues: 684 helix: 1.52 (0.34), residues: 215 sheet: 1.62 (0.37), residues: 194 loop : -0.80 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.002 0.001 HIS B 192 PHE 0.020 0.002 PHE C 216 TYR 0.012 0.001 TYR C 300 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: B 106 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: C 133 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7236 (tt) REVERT: C 204 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7405 (mp) REVERT: C 211 PHE cc_start: 0.7556 (t80) cc_final: 0.7183 (t80) REVERT: C 283 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7577 (t70) outliers start: 25 outliers final: 14 residues processed: 103 average time/residue: 0.9995 time to fit residues: 108.3083 Evaluate side-chains 101 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5531 Z= 0.219 Angle : 0.546 8.030 7536 Z= 0.284 Chirality : 0.042 0.177 893 Planarity : 0.004 0.042 921 Dihedral : 4.435 19.765 742 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.27 % Allowed : 17.73 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.00 (0.32), residues: 684 helix: 1.60 (0.34), residues: 215 sheet: 1.54 (0.37), residues: 196 loop : -0.78 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS B 201 PHE 0.013 0.001 PHE C 254 TYR 0.016 0.001 TYR C 132 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 0.539 Fit side-chains REVERT: B 106 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: C 133 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7221 (tt) REVERT: C 204 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7313 (mp) REVERT: C 211 PHE cc_start: 0.7450 (t80) cc_final: 0.7066 (t80) REVERT: C 283 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7548 (t70) outliers start: 26 outliers final: 14 residues processed: 99 average time/residue: 0.9699 time to fit residues: 101.0545 Evaluate side-chains 99 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5531 Z= 0.245 Angle : 0.565 8.271 7536 Z= 0.294 Chirality : 0.042 0.175 893 Planarity : 0.004 0.043 921 Dihedral : 4.424 19.664 742 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.78 % Allowed : 18.88 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.95 (0.32), residues: 684 helix: 1.56 (0.34), residues: 215 sheet: 1.49 (0.37), residues: 199 loop : -0.81 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.002 0.001 HIS C 292 PHE 0.029 0.001 PHE C 216 TYR 0.014 0.001 TYR C 218 ARG 0.008 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.654 Fit side-chains REVERT: B 106 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: C 133 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7262 (tt) REVERT: C 204 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7396 (mp) REVERT: C 211 PHE cc_start: 0.7458 (t80) cc_final: 0.7056 (t80) REVERT: C 283 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7545 (t70) outliers start: 23 outliers final: 14 residues processed: 98 average time/residue: 0.9386 time to fit residues: 97.1960 Evaluate side-chains 96 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5531 Z= 0.199 Angle : 0.557 7.924 7536 Z= 0.286 Chirality : 0.041 0.176 893 Planarity : 0.004 0.043 921 Dihedral : 4.336 19.469 742 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 19.54 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.03 (0.32), residues: 684 helix: 1.63 (0.34), residues: 215 sheet: 1.55 (0.37), residues: 196 loop : -0.75 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.001 0.000 HIS C 292 PHE 0.011 0.001 PHE C 290 TYR 0.019 0.001 TYR C 132 ARG 0.009 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.623 Fit side-chains REVERT: B 106 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: C 133 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7218 (tt) REVERT: C 204 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7367 (mp) REVERT: C 211 PHE cc_start: 0.7497 (t80) cc_final: 0.7089 (t80) REVERT: C 283 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7515 (t70) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.9733 time to fit residues: 98.4915 Evaluate side-chains 94 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5531 Z= 0.220 Angle : 0.572 8.573 7536 Z= 0.294 Chirality : 0.041 0.184 893 Planarity : 0.004 0.043 921 Dihedral : 4.325 19.254 742 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.96 % Allowed : 19.70 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.03 (0.32), residues: 684 helix: 1.59 (0.34), residues: 216 sheet: 1.56 (0.37), residues: 196 loop : -0.73 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS C 292 PHE 0.033 0.001 PHE C 216 TYR 0.013 0.001 TYR C 218 ARG 0.009 0.001 ARG C 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.825 Fit side-chains REVERT: B 106 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: C 133 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7237 (tt) REVERT: C 204 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7422 (mp) REVERT: C 211 PHE cc_start: 0.7458 (t80) cc_final: 0.7048 (t80) REVERT: C 283 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7452 (t70) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.9752 time to fit residues: 92.5722 Evaluate side-chains 94 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain C residue 283 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 76 ASN C 199 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.090495 restraints weight = 7754.449| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.65 r_work: 0.2984 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5531 Z= 0.195 Angle : 0.557 8.303 7536 Z= 0.288 Chirality : 0.041 0.152 893 Planarity : 0.004 0.042 921 Dihedral : 4.251 18.663 742 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.79 % Allowed : 19.87 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.11 (0.32), residues: 684 helix: 1.66 (0.34), residues: 216 sheet: 1.60 (0.37), residues: 196 loop : -0.69 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.000 HIS C 292 PHE 0.016 0.001 PHE C 254 TYR 0.021 0.001 TYR C 132 ARG 0.010 0.001 ARG C 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.22 seconds wall clock time: 41 minutes 42.70 seconds (2502.70 seconds total)