Starting phenix.real_space_refine on Sat May 10 14:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_41370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_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/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_41370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_41370.map" model { file = "/net/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_41370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tlm_41370/05_2025/8tlm_41370.cif" } 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.94, per 1000 atoms: 0.73 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 670.9 milliseconds 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: 0.65 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: 1.54 Time building geometry restraints manager: 1.58 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: 0.00 - 1.31: 7352 1.31 - 2.62: 149 2.62 - 3.93: 27 3.93 - 5.25: 7 5.25 - 6.56: 1 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 3.040 nonbonded pdb=" OG SER C 128 " pdb=" OH TYR C 218 " model vdw 2.063 3.040 nonbonded pdb=" O PHE C 122 " pdb=" OG1 THR C 125 " model vdw 2.258 3.040 nonbonded pdb=" OG SER A 212 " pdb=" OG1 THR A 214 " model vdw 2.330 3.040 nonbonded pdb=" NZ LYS C 107 " pdb=" O TYR C 172 " model vdw 2.386 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- 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 5536 Z= 0.129 Angle : 0.495 6.558 7546 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 Details of bonding type rmsd hydrogen bonds : bond 0.09412 ( 286) hydrogen bonds : angle 5.61635 ( 840) SS BOND : bond 0.00590 ( 5) SS BOND : angle 1.23832 ( 10) covalent geometry : bond 0.00275 ( 5531) covalent geometry : angle 0.49367 ( 7536) *********************** 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 to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.588 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: 1.1578 time to fit residues: 129.3268 Evaluate side-chains 87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.089966 restraints weight = 8039.034| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.70 r_work: 0.2925 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5536 Z= 0.144 Angle : 0.572 6.709 7546 Z= 0.299 Chirality : 0.043 0.161 893 Planarity : 0.004 0.042 921 Dihedral : 4.417 17.543 742 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.48 % Allowed : 10.02 % Favored : 88.51 % 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: 1.26 (0.32), residues: 684 helix: 1.65 (0.34), residues: 215 sheet: 1.59 (0.36), residues: 195 loop : -0.37 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS C 292 PHE 0.021 0.002 PHE C 254 TYR 0.014 0.001 TYR C 132 ARG 0.004 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 286) hydrogen bonds : angle 4.92391 ( 840) SS BOND : bond 0.00592 ( 5) SS BOND : angle 1.20956 ( 10) covalent geometry : bond 0.00339 ( 5531) covalent geometry : angle 0.57030 ( 7536) *********************** 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 97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.571 Fit side-chains REVERT: A 2 GLN cc_start: 0.8758 (mp10) cc_final: 0.8290 (mp10) REVERT: B 45 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 150 GLN cc_start: 0.7366 (mt0) cc_final: 0.6802 (mt0) REVERT: B 188 ASP cc_start: 0.8762 (m-30) cc_final: 0.8385 (p0) REVERT: B 190 GLU cc_start: 0.8488 (mp0) cc_final: 0.8285 (mp0) REVERT: B 214 ARG cc_start: 0.7279 (mtp85) cc_final: 0.6847 (mtm-85) REVERT: C 133 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6887 (tt) REVERT: C 195 LYS cc_start: 0.7894 (tttp) cc_final: 0.7683 (tttp) REVERT: C 216 PHE cc_start: 0.7505 (t80) cc_final: 0.7264 (t80) REVERT: C 283 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7478 (t70) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 1.1229 time to fit residues: 105.6393 Evaluate side-chains 87 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 159 LEU 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 21 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 53 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090511 restraints weight = 8048.987| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.73 r_work: 0.2941 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5536 Z= 0.121 Angle : 0.526 6.722 7546 Z= 0.277 Chirality : 0.041 0.166 893 Planarity : 0.003 0.042 921 Dihedral : 4.307 18.722 742 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.81 % Allowed : 12.32 % Favored : 85.88 % 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: 1.28 (0.32), residues: 684 helix: 1.70 (0.34), residues: 216 sheet: 1.68 (0.36), residues: 198 loop : -0.50 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 163 HIS 0.001 0.001 HIS B 201 PHE 0.013 0.001 PHE C 290 TYR 0.011 0.001 TYR C 132 ARG 0.005 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 286) hydrogen bonds : angle 4.68512 ( 840) SS BOND : bond 0.00517 ( 5) SS BOND : angle 1.04449 ( 10) covalent geometry : bond 0.00276 ( 5531) covalent geometry : angle 0.52462 ( 7536) *********************** 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 101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.620 Fit side-chains REVERT: A 2 GLN cc_start: 0.8766 (mp10) cc_final: 0.8360 (mp10) REVERT: A 77 ASP cc_start: 0.8322 (m-30) cc_final: 0.8079 (m-30) REVERT: B 45 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 150 GLN cc_start: 0.7314 (mt0) cc_final: 0.6774 (mt0) REVERT: B 188 ASP cc_start: 0.8751 (m-30) cc_final: 0.8420 (p0) REVERT: B 214 ARG cc_start: 0.7275 (mtp85) cc_final: 0.6869 (mtm-85) REVERT: C 133 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6938 (tt) REVERT: C 195 LYS cc_start: 0.7892 (tttp) cc_final: 0.7643 (tttp) REVERT: C 204 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7044 (mp) REVERT: C 216 PHE cc_start: 0.7424 (t80) cc_final: 0.7080 (t80) REVERT: C 283 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7544 (t70) outliers start: 11 outliers final: 3 residues processed: 94 average time/residue: 1.1007 time to fit residues: 108.3454 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 SER 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 283 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.089902 restraints weight = 8206.522| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.75 r_work: 0.2933 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5536 Z= 0.132 Angle : 0.531 6.774 7546 Z= 0.278 Chirality : 0.041 0.181 893 Planarity : 0.003 0.042 921 Dihedral : 4.285 18.678 742 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.30 % Allowed : 13.79 % Favored : 83.91 % 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: 1.27 (0.32), residues: 684 helix: 1.71 (0.34), residues: 216 sheet: 1.72 (0.37), residues: 198 loop : -0.56 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.001 0.001 HIS C 283 PHE 0.012 0.001 PHE C 290 TYR 0.015 0.001 TYR C 132 ARG 0.004 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 286) hydrogen bonds : angle 4.67226 ( 840) SS BOND : bond 0.00699 ( 5) SS BOND : angle 1.42890 ( 10) covalent geometry : bond 0.00308 ( 5531) covalent geometry : angle 0.52861 ( 7536) *********************** 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 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8739 (mp10) cc_final: 0.8277 (mp10) REVERT: B 45 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 127 GLN cc_start: 0.8307 (tt0) cc_final: 0.7753 (tt0) REVERT: C 133 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6931 (tt) REVERT: C 204 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 216 PHE cc_start: 0.7343 (t80) cc_final: 0.7008 (t80) REVERT: C 283 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7462 (t70) outliers start: 14 outliers final: 5 residues processed: 97 average time/residue: 1.0895 time to fit residues: 110.6186 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090408 restraints weight = 7999.373| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.71 r_work: 0.2937 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5536 Z= 0.118 Angle : 0.522 6.946 7546 Z= 0.273 Chirality : 0.041 0.168 893 Planarity : 0.003 0.042 921 Dihedral : 4.229 18.976 742 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.79 % Allowed : 14.94 % Favored : 82.27 % 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: 1.27 (0.32), residues: 684 helix: 1.75 (0.34), residues: 216 sheet: 1.73 (0.37), residues: 198 loop : -0.60 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.002 0.001 HIS C 292 PHE 0.012 0.001 PHE C 290 TYR 0.010 0.001 TYR B 49 ARG 0.004 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 286) hydrogen bonds : angle 4.59839 ( 840) SS BOND : bond 0.00616 ( 5) SS BOND : angle 1.25538 ( 10) covalent geometry : bond 0.00270 ( 5531) covalent geometry : angle 0.52053 ( 7536) *********************** 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 102 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 2 GLN cc_start: 0.8706 (mp10) cc_final: 0.8235 (mp10) REVERT: A 77 ASP cc_start: 0.8292 (m-30) cc_final: 0.8041 (m-30) REVERT: B 45 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 127 GLN cc_start: 0.8347 (tt0) cc_final: 0.7787 (tt0) REVERT: B 188 ASP cc_start: 0.8806 (m-30) cc_final: 0.8352 (p0) REVERT: C 133 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6871 (tt) REVERT: C 204 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7185 (mp) REVERT: C 216 PHE cc_start: 0.7334 (t80) cc_final: 0.6997 (t80) REVERT: C 283 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7487 (t70) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 1.0922 time to fit residues: 107.5154 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 181 THR Chi-restraints excluded: chain C residue 51 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088030 restraints weight = 8075.498| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.68 r_work: 0.2898 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5536 Z= 0.176 Angle : 0.567 7.286 7546 Z= 0.296 Chirality : 0.043 0.196 893 Planarity : 0.004 0.043 921 Dihedral : 4.451 19.093 742 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.94 % Allowed : 15.11 % Favored : 80.95 % 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: 1.16 (0.32), residues: 684 helix: 1.63 (0.34), residues: 215 sheet: 1.72 (0.37), residues: 197 loop : -0.68 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 47 HIS 0.003 0.001 HIS C 292 PHE 0.010 0.001 PHE A 92 TYR 0.015 0.001 TYR C 132 ARG 0.006 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 286) hydrogen bonds : angle 4.72647 ( 840) SS BOND : bond 0.00792 ( 5) SS BOND : angle 1.63897 ( 10) covalent geometry : bond 0.00424 ( 5531) covalent geometry : angle 0.56461 ( 7536) *********************** 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 114 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.620 Fit side-chains REVERT: A 2 GLN cc_start: 0.8758 (mp10) cc_final: 0.8363 (mp10) REVERT: A 153 ASP cc_start: 0.8317 (p0) cc_final: 0.7923 (p0) REVERT: B 45 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 188 ASP cc_start: 0.8800 (m-30) cc_final: 0.8293 (p0) REVERT: B 214 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6903 (mtm-85) REVERT: C 133 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6841 (tt) REVERT: C 211 PHE cc_start: 0.7109 (t80) cc_final: 0.6794 (t80) REVERT: C 216 PHE cc_start: 0.7314 (t80) cc_final: 0.7066 (t80) REVERT: C 283 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7486 (t70) outliers start: 24 outliers final: 13 residues processed: 102 average time/residue: 1.0669 time to fit residues: 114.0784 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 56 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 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 = 0.3529 r_free = 0.3529 target = 0.120482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.089664 restraints weight = 8013.631| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.73 r_work: 0.2933 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5536 Z= 0.126 Angle : 0.543 7.565 7546 Z= 0.281 Chirality : 0.041 0.182 893 Planarity : 0.003 0.042 921 Dihedral : 4.321 19.366 742 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.96 % Allowed : 16.42 % Favored : 80.62 % 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: 1.21 (0.32), residues: 684 helix: 1.72 (0.34), residues: 215 sheet: 1.77 (0.37), residues: 196 loop : -0.69 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.000 HIS B 192 PHE 0.009 0.001 PHE C 259 TYR 0.010 0.001 TYR B 49 ARG 0.006 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 286) hydrogen bonds : angle 4.62820 ( 840) SS BOND : bond 0.00630 ( 5) SS BOND : angle 1.20094 ( 10) covalent geometry : bond 0.00291 ( 5531) covalent geometry : angle 0.54197 ( 7536) *********************** 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 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.621 Fit side-chains REVERT: A 2 GLN cc_start: 0.8720 (mp10) cc_final: 0.8255 (mp10) REVERT: B 45 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 188 ASP cc_start: 0.8790 (m-30) cc_final: 0.8343 (p0) REVERT: B 214 ARG cc_start: 0.7316 (mtp85) cc_final: 0.7006 (mtm-85) REVERT: C 133 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7004 (tt) REVERT: C 216 PHE cc_start: 0.7373 (t80) cc_final: 0.7142 (t80) REVERT: C 283 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7527 (t70) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 1.0994 time to fit residues: 113.9072 Evaluate side-chains 97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 56 SER 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 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 14 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090221 restraints weight = 8079.136| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.74 r_work: 0.2945 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5536 Z= 0.120 Angle : 0.533 7.828 7546 Z= 0.276 Chirality : 0.041 0.167 893 Planarity : 0.004 0.043 921 Dihedral : 4.236 18.870 742 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 1.24 (0.32), residues: 684 helix: 1.71 (0.34), residues: 215 sheet: 1.81 (0.37), residues: 196 loop : -0.69 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS C 292 PHE 0.008 0.001 PHE C 259 TYR 0.017 0.001 TYR C 132 ARG 0.005 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 286) hydrogen bonds : angle 4.59017 ( 840) SS BOND : bond 0.00577 ( 5) SS BOND : angle 1.11552 ( 10) covalent geometry : bond 0.00277 ( 5531) covalent geometry : angle 0.53165 ( 7536) *********************** 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 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.585 Fit side-chains REVERT: A 2 GLN cc_start: 0.8715 (mp10) cc_final: 0.8356 (mp10) REVERT: A 77 ASP cc_start: 0.8303 (m-30) cc_final: 0.8074 (m-30) REVERT: B 45 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 188 ASP cc_start: 0.8792 (m-30) cc_final: 0.8330 (p0) REVERT: B 214 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6972 (mtm-85) REVERT: C 133 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7120 (tt) REVERT: C 216 PHE cc_start: 0.7319 (t80) cc_final: 0.7085 (t80) REVERT: C 283 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7606 (t70) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 1.2440 time to fit residues: 127.4625 Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 56 SER 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 214 PHE 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 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 0.0000 chunk 42 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.3382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091927 restraints weight = 8038.979| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.74 r_work: 0.2968 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5536 Z= 0.105 Angle : 0.532 7.996 7546 Z= 0.275 Chirality : 0.041 0.177 893 Planarity : 0.003 0.042 921 Dihedral : 4.096 18.554 742 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 18.39 % 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: 1.30 (0.32), residues: 684 helix: 1.77 (0.35), residues: 216 sheet: 1.80 (0.37), residues: 198 loop : -0.64 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 163 HIS 0.003 0.001 HIS B 192 PHE 0.008 0.001 PHE C 259 TYR 0.010 0.001 TYR B 49 ARG 0.006 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 286) hydrogen bonds : angle 4.51355 ( 840) SS BOND : bond 0.00472 ( 5) SS BOND : angle 0.95589 ( 10) covalent geometry : bond 0.00229 ( 5531) covalent geometry : angle 0.53165 ( 7536) *********************** 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 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.603 Fit side-chains REVERT: A 2 GLN cc_start: 0.8683 (mp10) cc_final: 0.8210 (mp10) REVERT: A 77 ASP cc_start: 0.8278 (m-30) cc_final: 0.7948 (m-30) REVERT: B 45 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 188 ASP cc_start: 0.8838 (m-30) cc_final: 0.8327 (p0) REVERT: B 214 ARG cc_start: 0.7313 (mtp85) cc_final: 0.6984 (mtm-85) REVERT: C 133 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7036 (tt) REVERT: C 216 PHE cc_start: 0.7250 (t80) cc_final: 0.6948 (t80) REVERT: C 283 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.7583 (t70) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 1.1176 time to fit residues: 108.9409 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 133 LEU 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 33 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089961 restraints weight = 8074.595| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.68 r_work: 0.2933 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5536 Z= 0.148 Angle : 0.566 8.160 7546 Z= 0.290 Chirality : 0.042 0.179 893 Planarity : 0.004 0.043 921 Dihedral : 4.240 18.492 742 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 18.56 % Favored : 79.64 % 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: 1.27 (0.32), residues: 684 helix: 1.71 (0.35), residues: 216 sheet: 1.82 (0.37), residues: 197 loop : -0.65 (0.37), residues: 271 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 0.015 0.001 PHE C 254 TYR 0.019 0.001 TYR C 132 ARG 0.005 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 286) hydrogen bonds : angle 4.57039 ( 840) SS BOND : bond 0.00644 ( 5) SS BOND : angle 1.27825 ( 10) covalent geometry : bond 0.00353 ( 5531) covalent geometry : angle 0.56411 ( 7536) ********************** 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 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.619 Fit side-chains REVERT: A 2 GLN cc_start: 0.8714 (mp10) cc_final: 0.8317 (mp10) REVERT: A 77 ASP cc_start: 0.8266 (m-30) cc_final: 0.8027 (m-30) REVERT: B 45 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 188 ASP cc_start: 0.8860 (m-30) cc_final: 0.8297 (p0) REVERT: C 133 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6966 (tt) REVERT: C 211 PHE cc_start: 0.7107 (t80) cc_final: 0.6775 (t80) REVERT: C 216 PHE cc_start: 0.7273 (t80) cc_final: 0.7003 (t80) REVERT: C 283 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7359 (t70) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 1.1106 time to fit residues: 112.8663 Evaluate side-chains 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 18 THR 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 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 41 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092897 restraints weight = 8032.210| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.66 r_work: 0.2976 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5536 Z= 0.110 Angle : 0.549 7.933 7546 Z= 0.282 Chirality : 0.041 0.180 893 Planarity : 0.003 0.042 921 Dihedral : 4.115 18.324 742 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.81 % Allowed : 18.56 % Favored : 79.64 % 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: 1.31 (0.32), residues: 684 helix: 1.74 (0.35), residues: 216 sheet: 1.83 (0.37), residues: 198 loop : -0.61 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 251 HIS 0.003 0.000 HIS C 292 PHE 0.008 0.001 PHE C 259 TYR 0.010 0.001 TYR B 49 ARG 0.009 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 286) hydrogen bonds : angle 4.48133 ( 840) SS BOND : bond 0.00500 ( 5) SS BOND : angle 0.94110 ( 10) covalent geometry : bond 0.00246 ( 5531) covalent geometry : angle 0.54817 ( 7536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3871.46 seconds wall clock time: 67 minutes 44.65 seconds (4064.65 seconds total)