Starting phenix.real_space_refine on Wed Sep 17 07:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3k_44143/09_2025/9b3k_44143.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.038 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 960 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 27 5.16 5 C 3940 2.51 5 N 972 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6063 Number of models: 1 Model: "" Number of chains: 3 Chain: "Z" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2833 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1687 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain breaks: 1 Chain: "L" Number of atoms: 1543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain breaks: 4 bond proxies already assigned to first conformer: 1563 Time building chain proxies: 2.08, per 1000 atoms: 0.34 Number of scatterers: 6063 At special positions: 0 Unit cell: (66.825, 65.175, 129.525, 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 27 16.00 O 1124 8.00 N 972 7.00 C 3940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 181 " - pdb=" SG CYS H 237 " distance=2.03 Simple disulfide: pdb=" SG CYS L 47 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " 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: 0.52 Conformation dependent library (CDL) restraints added in 458.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 46.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'Z' and resid 3 through 21 removed outlier: 3.561A pdb=" N GLY Z 20 " --> pdb=" O PHE Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 24 No H-bonds generated for 'chain 'Z' and resid 22 through 24' Processing helix chain 'Z' and resid 25 through 34 Processing helix chain 'Z' and resid 36 through 66 removed outlier: 4.217A pdb=" N PHE Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) Proline residue: Z 56 - end of helix Processing helix chain 'Z' and resid 66 through 88 removed outlier: 3.709A pdb=" N ILE Z 70 " --> pdb=" O GLY Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 119 Proline residue: Z 110 - end of helix Processing helix chain 'Z' and resid 124 through 150 Proline residue: Z 144 - end of helix Processing helix chain 'Z' and resid 156 through 177 Processing helix chain 'Z' and resid 204 through 224 removed outlier: 3.740A pdb=" N ALA Z 220 " --> pdb=" O PHE Z 216 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE Z 221 " --> pdb=" O GLY Z 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 234 removed outlier: 3.559A pdb=" N ASN Z 234 " --> pdb=" O ALA Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 258 Processing helix chain 'Z' and resid 258 through 266 Processing helix chain 'Z' and resid 267 through 288 Processing helix chain 'Z' and resid 291 through 302 removed outlier: 3.779A pdb=" N VAL Z 301 " --> pdb=" O LEU Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 321 removed outlier: 3.696A pdb=" N ARG Z 310 " --> pdb=" O PHE Z 306 " (cutoff:3.500A) Proline residue: Z 311 - end of helix Processing helix chain 'Z' and resid 324 through 352 Proline residue: Z 344 - end of helix removed outlier: 3.579A pdb=" N ALA Z 349 " --> pdb=" O LEU Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 384 Processing helix chain 'H' and resid 113 through 117 removed outlier: 3.672A pdb=" N THR H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.999A pdb=" N PHE L 107 " --> pdb=" O PRO L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 152 removed outlier: 3.689A pdb=" N GLY L 152 " --> pdb=" O GLN L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 212 removed outlier: 3.629A pdb=" N LYS L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 33 Processing sheet with id=AA2, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.637A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER H 78 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER H 58 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 84 through 86 removed outlier: 6.637A pdb=" N TRP H 62 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER H 76 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE H 60 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N SER H 78 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N SER H 58 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS H 122 " --> pdb=" O TRP H 145 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP H 145 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG H 124 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA H 132 " --> pdb=" O VAL H 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.785A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 161 through 165 removed outlier: 3.785A pdb=" N GLY H 180 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR H 217 " --> pdb=" O ASP H 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 191 through 195 removed outlier: 4.017A pdb=" N TYR H 235 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA8, first strand: chain 'L' and resid 34 through 37 removed outlier: 6.430A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 37 Processing sheet with id=AB1, first strand: chain 'L' and resid 140 through 142 removed outlier: 3.664A pdb=" N VAL L 157 " --> pdb=" O PHE L 142 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 169 through 169 Processing sheet with id=AB3, first strand: chain 'L' and resid 169 through 169 421 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1846 1.34 - 1.46: 1409 1.46 - 1.58: 2907 1.58 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 6207 Sorted by residual: bond pdb=" C VAL H 135 " pdb=" N GLY H 136 " ideal model delta sigma weight residual 1.328 1.310 0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" N TRP H 133 " pdb=" CA TRP H 133 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.12e+00 bond pdb=" CB ASP H 143 " pdb=" CG ASP H 143 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.04e+00 bond pdb=" CG PRO Z 311 " pdb=" CD PRO Z 311 " ideal model delta sigma weight residual 1.503 1.475 0.028 3.40e-02 8.65e+02 6.92e-01 bond pdb=" CB PRO Z 207 " pdb=" CG PRO Z 207 " ideal model delta sigma weight residual 1.492 1.452 0.040 5.00e-02 4.00e+02 6.28e-01 ... (remaining 6202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 8250 1.71 - 3.42: 141 3.42 - 5.13: 19 5.13 - 6.85: 10 6.85 - 8.56: 1 Bond angle restraints: 8421 Sorted by residual: angle pdb=" N VAL Z 153 " pdb=" CA VAL Z 153 " pdb=" C VAL Z 153 " ideal model delta sigma weight residual 112.96 108.86 4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N GLU H 189 " pdb=" CA GLU H 189 " pdb=" C GLU H 189 " ideal model delta sigma weight residual 109.81 116.19 -6.38 2.21e+00 2.05e-01 8.34e+00 angle pdb=" N VAL H 135 " pdb=" CA VAL H 135 " pdb=" C VAL H 135 " ideal model delta sigma weight residual 109.34 103.45 5.89 2.08e+00 2.31e-01 8.02e+00 angle pdb=" C TRP H 133 " pdb=" CA TRP H 133 " pdb=" CB TRP H 133 " ideal model delta sigma weight residual 110.42 116.05 -5.63 1.99e+00 2.53e-01 8.00e+00 angle pdb=" CA LEU L 199 " pdb=" CB LEU L 199 " pdb=" CG LEU L 199 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 ... (remaining 8416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3134 17.86 - 35.71: 362 35.71 - 53.57: 101 53.57 - 71.43: 26 71.43 - 89.28: 6 Dihedral angle restraints: 3629 sinusoidal: 1351 harmonic: 2278 Sorted by residual: dihedral pdb=" CB CYS H 181 " pdb=" SG CYS H 181 " pdb=" SG CYS H 237 " pdb=" CB CYS H 237 " ideal model delta sinusoidal sigma weight residual -86.00 -149.73 63.73 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA GLU H 189 " pdb=" C GLU H 189 " pdb=" N PRO H 190 " pdb=" CA PRO H 190 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CB CYS H 48 " pdb=" SG CYS H 48 " pdb=" SG CYS H 122 " pdb=" CB CYS H 122 " ideal model delta sinusoidal sigma weight residual 93.00 58.29 34.71 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 3626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 719 0.043 - 0.086: 184 0.086 - 0.129: 57 0.129 - 0.172: 5 0.172 - 0.215: 2 Chirality restraints: 967 Sorted by residual: chirality pdb=" CB VAL Z 233 " pdb=" CA VAL Z 233 " pdb=" CG1 VAL Z 233 " pdb=" CG2 VAL Z 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR Z 206 " pdb=" N THR Z 206 " pdb=" C THR Z 206 " pdb=" CB THR Z 206 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB THR Z 206 " pdb=" CA THR Z 206 " pdb=" OG1 THR Z 206 " pdb=" CG2 THR Z 206 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 964 not shown) Planarity restraints: 1045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 189 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO H 190 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 190 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 190 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 135 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C VAL H 135 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL H 135 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY H 136 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 132 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ALA H 132 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA H 132 " 0.009 2.00e-02 2.50e+03 pdb=" N TRP H 133 " 0.008 2.00e-02 2.50e+03 ... (remaining 1042 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 470 2.74 - 3.28: 5767 3.28 - 3.82: 10480 3.82 - 4.36: 12452 4.36 - 4.90: 21514 Nonbonded interactions: 50683 Sorted by model distance: nonbonded pdb=" O SER H 81 " pdb=" OG SER H 81 " model vdw 2.195 3.040 nonbonded pdb=" OD2 ASP L 194 " pdb=" OG1 THR L 196 " model vdw 2.231 3.040 nonbonded pdb=" O SER H 111 " pdb=" OG SER H 111 " model vdw 2.243 3.040 nonbonded pdb=" OG SER Z 81 " pdb=" O SER Z 97 " model vdw 2.276 3.040 nonbonded pdb=" O SER L 54 " pdb=" NH2 ARG L 90 " model vdw 2.290 3.120 ... (remaining 50678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.12 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: 4.170 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.600 Find NCS groups from input model: 0.030 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.004 0.040 6211 Z= 0.176 Angle : 0.586 8.558 8429 Z= 0.305 Chirality : 0.043 0.215 967 Planarity : 0.004 0.044 1045 Dihedral : 17.050 89.284 2165 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.35 % Allowed : 24.02 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.31), residues: 780 helix: 2.26 (0.29), residues: 343 sheet: 1.21 (0.36), residues: 207 loop : -0.92 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 64 TYR 0.011 0.002 TYR H 121 PHE 0.021 0.002 PHE Z 335 TRP 0.010 0.001 TRP H 139 HIS 0.002 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6207) covalent geometry : angle 0.58552 ( 8421) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.68730 ( 8) hydrogen bonds : bond 0.10059 ( 385) hydrogen bonds : angle 5.22859 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.241 Fit side-chains REVERT: L 48 ARG cc_start: 0.7132 (mpt90) cc_final: 0.6915 (mmt180) outliers start: 29 outliers final: 28 residues processed: 103 average time/residue: 0.5098 time to fit residues: 55.4373 Evaluate side-chains 102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 79 SER Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 229 THR Chi-restraints excluded: chain Z residue 267 SER Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 200 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 128 ASN ** H 241 HIS ** 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 = 0.3927 r_free = 0.3927 target = 0.162957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117281 restraints weight = 7930.265| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.37 r_work: 0.3123 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6211 Z= 0.137 Angle : 0.556 8.388 8429 Z= 0.290 Chirality : 0.041 0.172 967 Planarity : 0.004 0.045 1045 Dihedral : 7.145 53.232 879 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.75 % Allowed : 22.52 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.31), residues: 780 helix: 2.55 (0.29), residues: 343 sheet: 1.46 (0.37), residues: 197 loop : -0.92 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.010 0.001 TYR H 121 PHE 0.017 0.001 PHE Z 16 TRP 0.012 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6207) covalent geometry : angle 0.55647 ( 8421) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.54330 ( 8) hydrogen bonds : bond 0.04084 ( 385) hydrogen bonds : angle 4.23744 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.261 Fit side-chains REVERT: Z 361 MET cc_start: 0.8718 (mtp) cc_final: 0.8512 (mtp) REVERT: H 91 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7499 (tmtt) REVERT: H 154 PHE cc_start: 0.6647 (m-80) cc_final: 0.6307 (m-10) REVERT: L 48 ARG cc_start: 0.7537 (mpt90) cc_final: 0.7183 (mmt180) outliers start: 25 outliers final: 12 residues processed: 92 average time/residue: 0.5727 time to fit residues: 55.3300 Evaluate side-chains 82 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104324 restraints weight = 11742.852| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.31 r_work: 0.3060 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6211 Z= 0.176 Angle : 0.580 6.577 8429 Z= 0.303 Chirality : 0.043 0.180 967 Planarity : 0.004 0.047 1045 Dihedral : 6.225 53.736 857 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.75 % Allowed : 22.52 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.31), residues: 780 helix: 2.38 (0.28), residues: 344 sheet: 1.44 (0.38), residues: 196 loop : -0.99 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.011 0.002 TYR H 121 PHE 0.021 0.002 PHE Z 335 TRP 0.009 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6207) covalent geometry : angle 0.57970 ( 8421) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.60096 ( 8) hydrogen bonds : bond 0.04593 ( 385) hydrogen bonds : angle 4.26616 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.233 Fit side-chains REVERT: H 72 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: H 154 PHE cc_start: 0.6633 (m-80) cc_final: 0.6228 (m-10) REVERT: L 48 ARG cc_start: 0.7581 (mpt90) cc_final: 0.7233 (mmt180) REVERT: L 199 LEU cc_start: 0.8064 (tt) cc_final: 0.7747 (tm) outliers start: 25 outliers final: 16 residues processed: 93 average time/residue: 0.5678 time to fit residues: 55.4495 Evaluate side-chains 88 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107660 restraints weight = 15435.913| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.37 r_work: 0.3059 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6211 Z= 0.118 Angle : 0.527 6.477 8429 Z= 0.275 Chirality : 0.041 0.208 967 Planarity : 0.004 0.045 1045 Dihedral : 5.857 52.250 857 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.60 % Allowed : 23.12 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.31), residues: 780 helix: 2.61 (0.29), residues: 345 sheet: 1.45 (0.37), residues: 197 loop : -0.86 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.009 0.001 TYR H 121 PHE 0.015 0.001 PHE Z 16 TRP 0.007 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6207) covalent geometry : angle 0.52659 ( 8421) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.49598 ( 8) hydrogen bonds : bond 0.03664 ( 385) hydrogen bonds : angle 4.04188 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.288 Fit side-chains REVERT: Z 310 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7255 (mtt180) REVERT: H 91 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7470 (tmtt) REVERT: H 154 PHE cc_start: 0.6359 (m-80) cc_final: 0.5922 (m-10) REVERT: L 48 ARG cc_start: 0.7521 (mpt90) cc_final: 0.7190 (mmt180) REVERT: L 199 LEU cc_start: 0.7880 (tt) cc_final: 0.7518 (tm) outliers start: 24 outliers final: 13 residues processed: 94 average time/residue: 0.5223 time to fit residues: 51.8099 Evaluate side-chains 87 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119590 restraints weight = 9520.732| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.86 r_work: 0.3131 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6211 Z= 0.114 Angle : 0.516 6.474 8429 Z= 0.269 Chirality : 0.040 0.185 967 Planarity : 0.004 0.044 1045 Dihedral : 5.388 53.017 851 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.05 % Allowed : 22.82 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.31), residues: 780 helix: 2.67 (0.29), residues: 345 sheet: 1.49 (0.37), residues: 197 loop : -0.84 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.009 0.001 TYR H 121 PHE 0.015 0.001 PHE Z 335 TRP 0.006 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6207) covalent geometry : angle 0.51645 ( 8421) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.47512 ( 8) hydrogen bonds : bond 0.03546 ( 385) hydrogen bonds : angle 3.96709 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.164 Fit side-chains REVERT: Z 157 MET cc_start: 0.7965 (tpp) cc_final: 0.7570 (tpp) REVERT: Z 269 LEU cc_start: 0.8262 (mt) cc_final: 0.8028 (mm) REVERT: Z 310 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: H 91 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7457 (tmtt) REVERT: L 48 ARG cc_start: 0.7541 (mpt90) cc_final: 0.7220 (mmt180) REVERT: L 199 LEU cc_start: 0.8053 (tt) cc_final: 0.7693 (tm) outliers start: 27 outliers final: 15 residues processed: 99 average time/residue: 0.5375 time to fit residues: 55.9566 Evaluate side-chains 93 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105709 restraints weight = 11798.239| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.32 r_work: 0.3084 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6211 Z= 0.148 Angle : 0.556 7.703 8429 Z= 0.287 Chirality : 0.042 0.178 967 Planarity : 0.005 0.087 1045 Dihedral : 5.456 52.754 850 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.75 % Allowed : 23.57 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.31), residues: 780 helix: 2.56 (0.28), residues: 344 sheet: 1.46 (0.37), residues: 197 loop : -0.95 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.010 0.001 TYR H 121 PHE 0.020 0.002 PHE Z 335 TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6207) covalent geometry : angle 0.55646 ( 8421) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.52046 ( 8) hydrogen bonds : bond 0.04110 ( 385) hydrogen bonds : angle 4.07917 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.240 Fit side-chains REVERT: Z 269 LEU cc_start: 0.8308 (mt) cc_final: 0.8078 (mm) REVERT: Z 310 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7438 (mtt180) REVERT: H 72 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: H 91 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7455 (tmtt) REVERT: H 102 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7533 (pmtt) REVERT: L 48 ARG cc_start: 0.7546 (mpt90) cc_final: 0.7206 (mmt180) REVERT: L 199 LEU cc_start: 0.8083 (tt) cc_final: 0.7706 (tm) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.5426 time to fit residues: 52.5432 Evaluate side-chains 95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116394 restraints weight = 7945.101| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.31 r_work: 0.3117 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6211 Z= 0.153 Angle : 0.562 7.426 8429 Z= 0.291 Chirality : 0.042 0.179 967 Planarity : 0.005 0.091 1045 Dihedral : 5.488 52.584 850 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.50 % Allowed : 22.82 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.31), residues: 780 helix: 2.49 (0.28), residues: 346 sheet: 1.47 (0.37), residues: 196 loop : -0.92 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.011 0.001 TYR H 121 PHE 0.020 0.002 PHE Z 335 TRP 0.008 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6207) covalent geometry : angle 0.56238 ( 8421) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.53371 ( 8) hydrogen bonds : bond 0.04215 ( 385) hydrogen bonds : angle 4.11059 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.243 Fit side-chains REVERT: Z 157 MET cc_start: 0.8029 (tpp) cc_final: 0.7736 (tpp) REVERT: Z 269 LEU cc_start: 0.8345 (mt) cc_final: 0.8096 (mm) REVERT: Z 310 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7391 (mtt180) REVERT: H 72 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: H 91 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7442 (tmtt) REVERT: H 102 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7522 (pmtt) REVERT: H 154 PHE cc_start: 0.6625 (m-80) cc_final: 0.6268 (m-10) REVERT: L 48 ARG cc_start: 0.7545 (mpt90) cc_final: 0.7202 (mmt180) REVERT: L 199 LEU cc_start: 0.8020 (tt) cc_final: 0.7646 (tm) outliers start: 30 outliers final: 19 residues processed: 98 average time/residue: 0.5365 time to fit residues: 55.3874 Evaluate side-chains 95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 297 LEU Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116672 restraints weight = 8224.740| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.41 r_work: 0.3119 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6211 Z= 0.140 Angle : 0.554 7.219 8429 Z= 0.287 Chirality : 0.042 0.225 967 Planarity : 0.005 0.090 1045 Dihedral : 5.465 52.569 850 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.90 % Allowed : 23.72 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.31), residues: 780 helix: 2.50 (0.29), residues: 346 sheet: 1.43 (0.37), residues: 197 loop : -0.91 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.010 0.001 TYR H 121 PHE 0.019 0.001 PHE Z 335 TRP 0.008 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6207) covalent geometry : angle 0.55443 ( 8421) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.50041 ( 8) hydrogen bonds : bond 0.04042 ( 385) hydrogen bonds : angle 4.08425 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.296 Fit side-chains REVERT: Z 269 LEU cc_start: 0.8326 (mt) cc_final: 0.8082 (mm) REVERT: Z 310 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7385 (mtt180) REVERT: H 91 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7432 (tmtt) REVERT: H 102 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7516 (pmtt) REVERT: H 154 PHE cc_start: 0.6639 (m-80) cc_final: 0.6252 (m-10) REVERT: L 48 ARG cc_start: 0.7530 (mpt90) cc_final: 0.7188 (mmt180) REVERT: L 124 GLN cc_start: 0.8308 (tt0) cc_final: 0.7876 (pp30) REVERT: L 199 LEU cc_start: 0.8014 (tt) cc_final: 0.7633 (tm) outliers start: 26 outliers final: 19 residues processed: 94 average time/residue: 0.5317 time to fit residues: 52.6904 Evaluate side-chains 95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 153 VAL Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 297 LEU Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118105 restraints weight = 9537.855| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.85 r_work: 0.3108 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6211 Z= 0.132 Angle : 0.544 7.032 8429 Z= 0.281 Chirality : 0.041 0.218 967 Planarity : 0.005 0.093 1045 Dihedral : 5.397 52.445 850 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.20 % Allowed : 23.42 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.31), residues: 780 helix: 2.57 (0.29), residues: 345 sheet: 1.46 (0.37), residues: 197 loop : -0.88 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.010 0.001 TYR H 121 PHE 0.017 0.001 PHE Z 335 TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6207) covalent geometry : angle 0.54382 ( 8421) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.48337 ( 8) hydrogen bonds : bond 0.03873 ( 385) hydrogen bonds : angle 4.03191 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: Z 269 LEU cc_start: 0.8282 (mt) cc_final: 0.8051 (mm) REVERT: Z 310 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7406 (mtt180) REVERT: H 72 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: H 91 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7441 (tmtt) REVERT: H 154 PHE cc_start: 0.6511 (m-80) cc_final: 0.6074 (m-10) REVERT: L 48 ARG cc_start: 0.7535 (mpt90) cc_final: 0.7201 (mmt180) REVERT: L 124 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: L 199 LEU cc_start: 0.8064 (tt) cc_final: 0.7684 (tm) outliers start: 28 outliers final: 21 residues processed: 95 average time/residue: 0.5452 time to fit residues: 54.4866 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 12 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 297 LEU Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.0060 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121371 restraints weight = 9491.940| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.80 r_work: 0.3170 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6211 Z= 0.103 Angle : 0.519 6.685 8429 Z= 0.268 Chirality : 0.040 0.204 967 Planarity : 0.004 0.092 1045 Dihedral : 5.228 51.605 850 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.00 % Allowed : 24.47 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.31), residues: 780 helix: 2.77 (0.29), residues: 345 sheet: 1.54 (0.37), residues: 196 loop : -0.84 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 134 TYR 0.009 0.001 TYR H 121 PHE 0.012 0.001 PHE Z 16 TRP 0.005 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6207) covalent geometry : angle 0.51874 ( 8421) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.44095 ( 8) hydrogen bonds : bond 0.03183 ( 385) hydrogen bonds : angle 3.88152 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.247 Fit side-chains REVERT: Z 157 MET cc_start: 0.7889 (tpp) cc_final: 0.7483 (tpp) REVERT: Z 310 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7273 (mtt180) REVERT: H 91 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7408 (tmtt) REVERT: H 102 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7322 (pmtt) REVERT: H 154 PHE cc_start: 0.6299 (m-80) cc_final: 0.5879 (m-10) REVERT: L 48 ARG cc_start: 0.7559 (mpt90) cc_final: 0.6916 (mmt90) REVERT: L 124 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7780 (pp30) REVERT: L 199 LEU cc_start: 0.8040 (tt) cc_final: 0.7677 (tm) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.5559 time to fit residues: 53.6329 Evaluate side-chains 91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 309 ILE Chi-restraints excluded: chain Z residue 310 ARG Chi-restraints excluded: chain Z residue 353 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 102 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 0.0970 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118085 restraints weight = 6356.003| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.92 r_work: 0.3169 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6211 Z= 0.123 Angle : 0.543 6.810 8429 Z= 0.279 Chirality : 0.041 0.205 967 Planarity : 0.005 0.093 1045 Dihedral : 5.194 50.715 849 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 24.77 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.31), residues: 780 helix: 2.72 (0.29), residues: 345 sheet: 1.55 (0.38), residues: 196 loop : -0.84 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 380 TYR 0.010 0.001 TYR H 121 PHE 0.017 0.001 PHE Z 335 TRP 0.006 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6207) covalent geometry : angle 0.54287 ( 8421) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.47318 ( 8) hydrogen bonds : bond 0.03613 ( 385) hydrogen bonds : angle 3.92444 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3014.72 seconds wall clock time: 52 minutes 7.74 seconds (3127.74 seconds total)