Starting phenix.real_space_refine on Mon Apr 28 02:36:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3k_44143/04_2025/9b3k_44143.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3k_44143/04_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_44143/04_2025/9b3k_44143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3k_44143/04_2025/9b3k_44143.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3k_44143/04_2025/9b3k_44143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3k_44143/04_2025/9b3k_44143.cif" } resolution = 2.56 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= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.51, per 1000 atoms: 0.91 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: 1.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.72 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: 1.96 Time building geometry restraints manager: 1.78 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- 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 (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: 1.63 (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 TRP 0.010 0.001 TRP H 139 HIS 0.002 0.001 HIS H 241 PHE 0.021 0.002 PHE Z 335 TYR 0.011 0.002 TYR H 121 ARG 0.002 0.000 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.10059 ( 385) hydrogen bonds : angle 5.22859 ( 1182) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.68730 ( 8) covalent geometry : bond 0.00414 ( 6207) covalent geometry : angle 0.58552 ( 8421) *********************** 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 : 0.644 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: 0.9984 time to fit residues: 109.0170 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 : 0.719 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.2980 chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117474 restraints weight = 7887.503| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.35 r_work: 0.3127 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- 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 = 0.12 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0571 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= 0.133 Angle : 0.554 8.353 8429 Z= 0.289 Chirality : 0.041 0.169 967 Planarity : 0.004 0.045 1045 Dihedral : 7.158 53.633 879 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.60 % Allowed : 22.67 % 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 (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: 1.89 (0.31), residues: 780 helix: 2.54 (0.29), residues: 344 sheet: 1.45 (0.37), residues: 197 loop : -0.93 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 PHE 0.017 0.001 PHE Z 335 TYR 0.010 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 385) hydrogen bonds : angle 4.22977 ( 1182) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.55307 ( 8) covalent geometry : bond 0.00303 ( 6207) covalent geometry : angle 0.55368 ( 8421) *********************** 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: 24 poor density : 72 time to evaluate : 0.674 Fit side-chains REVERT: L 48 ARG cc_start: 0.7524 (mpt90) cc_final: 0.7182 (mmt180) outliers start: 24 outliers final: 12 residues processed: 93 average time/residue: 1.1673 time to fit residues: 114.3772 Evaluate side-chains 81 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 0.0070 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.165340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119972 restraints weight = 7896.651| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.36 r_work: 0.3170 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.76 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: 0.8385 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6211 Z= 0.109 Angle : 0.515 6.307 8429 Z= 0.268 Chirality : 0.040 0.166 967 Planarity : 0.004 0.043 1045 Dihedral : 5.747 54.862 857 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.00 % Allowed : 23.27 % 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 (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: 2.04 (0.31), residues: 780 helix: 2.65 (0.29), residues: 345 sheet: 1.49 (0.37), residues: 197 loop : -0.81 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 133 HIS 0.003 0.001 HIS Z 155 PHE 0.014 0.001 PHE Z 16 TYR 0.009 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 385) hydrogen bonds : angle 4.01496 ( 1182) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.47852 ( 8) covalent geometry : bond 0.00240 ( 6207) covalent geometry : angle 0.51544 ( 8421) *********************** 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 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.639 Fit side-chains REVERT: Z 269 LEU cc_start: 0.8233 (mt) cc_final: 0.8027 (mm) REVERT: H 91 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7451 (tmtt) REVERT: H 154 PHE cc_start: 0.6414 (m-80) cc_final: 0.6042 (m-10) REVERT: L 48 ARG cc_start: 0.7479 (mpt90) cc_final: 0.6835 (mmt90) REVERT: L 199 LEU cc_start: 0.7998 (tt) cc_final: 0.7686 (tm) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 1.0390 time to fit residues: 105.7912 Evaluate side-chains 90 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 140 PHE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 297 LEU 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 L residue 57 VAL Chi-restraints excluded: chain L residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.0040 chunk 78 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.163381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117929 restraints weight = 9497.731| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.79 r_work: 0.3110 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0822 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= 0.136 Angle : 0.538 6.475 8429 Z= 0.281 Chirality : 0.041 0.201 967 Planarity : 0.004 0.082 1045 Dihedral : 5.495 52.686 851 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.35 % Allowed : 22.52 % 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 (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: 1.96 (0.31), residues: 780 helix: 2.60 (0.29), residues: 344 sheet: 1.49 (0.37), residues: 197 loop : -0.91 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.020 0.001 PHE Z 335 TYR 0.010 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 385) hydrogen bonds : angle 4.07487 ( 1182) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.52870 ( 8) covalent geometry : bond 0.00316 ( 6207) covalent geometry : angle 0.53778 ( 8421) *********************** 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 105 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.650 Fit side-chains REVERT: Z 269 LEU cc_start: 0.8295 (mt) cc_final: 0.8056 (mm) REVERT: H 72 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8679 (tt0) REVERT: H 91 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7465 (tmtt) REVERT: H 154 PHE cc_start: 0.6499 (m-80) cc_final: 0.6079 (m-10) REVERT: L 48 ARG cc_start: 0.7525 (mpt90) cc_final: 0.6880 (mmt90) REVERT: L 199 LEU cc_start: 0.8026 (tt) cc_final: 0.7683 (tm) outliers start: 29 outliers final: 14 residues processed: 97 average time/residue: 1.0485 time to fit residues: 107.5568 Evaluate side-chains 89 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 206 THR Chi-restraints excluded: chain Z residue 209 ILE Chi-restraints excluded: chain Z residue 287 VAL 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 91 LYS 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 57 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 124 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.163708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117929 restraints weight = 8236.648| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.43 r_work: 0.3138 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0890 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= 0.126 Angle : 0.528 6.456 8429 Z= 0.275 Chirality : 0.041 0.187 967 Planarity : 0.004 0.076 1045 Dihedral : 5.455 52.537 851 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.50 % Allowed : 21.92 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.00 (0.31), residues: 780 helix: 2.61 (0.28), residues: 345 sheet: 1.47 (0.38), residues: 197 loop : -0.82 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.017 0.001 PHE Z 335 TYR 0.010 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 385) hydrogen bonds : angle 4.01821 ( 1182) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.47627 ( 8) covalent geometry : bond 0.00288 ( 6207) covalent geometry : angle 0.52766 ( 8421) *********************** 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: 30 poor density : 75 time to evaluate : 0.686 Fit side-chains REVERT: Z 310 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: H 72 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: H 91 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7476 (tmtt) REVERT: L 48 ARG cc_start: 0.7516 (mpt90) cc_final: 0.6905 (mmt90) REVERT: L 199 LEU cc_start: 0.7996 (tt) cc_final: 0.7641 (tm) outliers start: 30 outliers final: 20 residues processed: 96 average time/residue: 1.0559 time to fit residues: 107.2341 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 : 0.659 ------------------------------------------------------------------------------- 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 287 VAL 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 38 VAL Chi-restraints excluded: chain H residue 69 LYS 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 111 SER Chi-restraints excluded: chain H residue 117 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 57 VAL Chi-restraints excluded: chain L residue 124 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.163909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117009 restraints weight = 6260.029| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.92 r_work: 0.3157 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6211 Z= 0.123 Angle : 0.535 6.463 8429 Z= 0.276 Chirality : 0.041 0.175 967 Planarity : 0.004 0.067 1045 Dihedral : 5.365 52.315 850 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.65 % Allowed : 22.07 % 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 (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: 2.01 (0.31), residues: 780 helix: 2.63 (0.28), residues: 345 sheet: 1.49 (0.38), residues: 197 loop : -0.83 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.017 0.001 PHE Z 335 TYR 0.010 0.001 TYR H 121 ARG 0.002 0.000 ARG Z 380 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 385) hydrogen bonds : angle 4.00022 ( 1182) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.47267 ( 8) covalent geometry : bond 0.00281 ( 6207) covalent geometry : angle 0.53476 ( 8421) *********************** 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 106 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 1.777 Fit side-chains REVERT: Z 310 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7351 (mtt180) REVERT: H 72 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: H 91 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7479 (tmtt) REVERT: L 48 ARG cc_start: 0.7549 (mpt90) cc_final: 0.6929 (mmt90) REVERT: L 199 LEU cc_start: 0.8076 (tt) cc_final: 0.7718 (tm) outliers start: 31 outliers final: 20 residues processed: 96 average time/residue: 1.4923 time to fit residues: 152.6691 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 : 0.804 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain Z residue 297 LEU 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.160553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.115216 restraints weight = 7862.798| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.35 r_work: 0.3086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6211 Z= 0.205 Angle : 0.611 7.990 8429 Z= 0.316 Chirality : 0.044 0.185 967 Planarity : 0.005 0.070 1045 Dihedral : 5.561 54.994 849 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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 (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: 1.70 (0.31), residues: 780 helix: 2.36 (0.28), residues: 344 sheet: 1.42 (0.37), residues: 196 loop : -1.02 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.024 0.002 PHE Z 335 TYR 0.013 0.002 TYR H 121 ARG 0.002 0.000 ARG Z 380 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 385) hydrogen bonds : angle 4.28340 ( 1182) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.61076 ( 8) covalent geometry : bond 0.00492 ( 6207) covalent geometry : angle 0.61093 ( 8421) *********************** 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 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.692 Fit side-chains REVERT: Z 310 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7434 (mtt180) REVERT: H 72 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: H 91 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7471 (tmtt) REVERT: H 154 PHE cc_start: 0.6637 (m-80) cc_final: 0.6295 (m-10) REVERT: L 33 SER cc_start: 0.8176 (t) cc_final: 0.7742 (p) REVERT: L 48 ARG cc_start: 0.7591 (mpt90) cc_final: 0.7245 (mmt180) REVERT: L 199 LEU cc_start: 0.8007 (tt) cc_final: 0.7639 (tm) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 1.0495 time to fit residues: 104.3446 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 : 0.675 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.163492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117644 restraints weight = 8178.608| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.42 r_work: 0.3137 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0929 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= 0.122 Angle : 0.544 7.241 8429 Z= 0.280 Chirality : 0.041 0.176 967 Planarity : 0.004 0.064 1045 Dihedral : 5.316 51.702 849 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.45 % Allowed : 23.27 % 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 (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: 1.93 (0.31), residues: 780 helix: 2.58 (0.29), residues: 345 sheet: 1.44 (0.38), residues: 197 loop : -0.92 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.017 0.001 PHE Z 16 TYR 0.010 0.001 TYR H 121 ARG 0.002 0.000 ARG Z 380 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 385) hydrogen bonds : angle 4.03237 ( 1182) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.46814 ( 8) covalent geometry : bond 0.00272 ( 6207) covalent geometry : angle 0.54372 ( 8421) *********************** 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 94 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.662 Fit side-chains REVERT: Z 310 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7361 (mtt180) REVERT: H 91 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7500 (tmtt) REVERT: H 154 PHE cc_start: 0.6587 (m-80) cc_final: 0.6204 (m-10) REVERT: L 48 ARG cc_start: 0.7565 (mpt90) cc_final: 0.7214 (mmt180) REVERT: L 199 LEU cc_start: 0.7992 (tt) cc_final: 0.7625 (tm) outliers start: 23 outliers final: 16 residues processed: 88 average time/residue: 1.1694 time to fit residues: 108.8603 Evaluate side-chains 88 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 76 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.161744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116400 restraints weight = 8190.537| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.44 r_work: 0.3104 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0855 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= 0.166 Angle : 0.577 7.298 8429 Z= 0.298 Chirality : 0.042 0.180 967 Planarity : 0.004 0.066 1045 Dihedral : 5.397 52.811 849 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.15 % Allowed : 23.87 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.81 (0.31), residues: 780 helix: 2.49 (0.28), residues: 344 sheet: 1.44 (0.37), residues: 196 loop : -1.02 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.022 0.002 PHE Z 335 TYR 0.011 0.002 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 385) hydrogen bonds : angle 4.13909 ( 1182) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.53763 ( 8) covalent geometry : bond 0.00393 ( 6207) covalent geometry : angle 0.57717 ( 8421) *********************** 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 92 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.731 Fit side-chains REVERT: Z 310 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7455 (mtt180) REVERT: H 91 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7472 (tmtt) REVERT: H 154 PHE cc_start: 0.6615 (m-80) cc_final: 0.6190 (m-10) REVERT: L 48 ARG cc_start: 0.7539 (mpt90) cc_final: 0.7195 (mmt180) REVERT: L 124 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7890 (pp30) REVERT: L 199 LEU cc_start: 0.7999 (tt) cc_final: 0.7616 (tm) outliers start: 21 outliers final: 18 residues processed: 87 average time/residue: 1.3579 time to fit residues: 124.9012 Evaluate side-chains 91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 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 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 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 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119165 restraints weight = 9779.866| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.08 r_work: 0.3113 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0994 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= 0.121 Angle : 0.542 7.001 8429 Z= 0.280 Chirality : 0.041 0.233 967 Planarity : 0.004 0.063 1045 Dihedral : 5.253 51.381 849 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 24.02 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.00 (0.31), residues: 780 helix: 2.66 (0.29), residues: 345 sheet: 1.48 (0.38), residues: 197 loop : -0.90 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.016 0.001 PHE Z 16 TYR 0.009 0.001 TYR H 121 ARG 0.002 0.000 ARG H 134 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 385) hydrogen bonds : angle 3.98352 ( 1182) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.48524 ( 8) covalent geometry : bond 0.00272 ( 6207) covalent geometry : angle 0.54230 ( 8421) ********************** 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 93 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.641 Fit side-chains REVERT: Z 310 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7374 (mtt180) REVERT: H 91 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7493 (tmtt) REVERT: H 102 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7362 (pmtt) REVERT: H 154 PHE cc_start: 0.6609 (m-80) cc_final: 0.6223 (m-10) REVERT: L 48 ARG cc_start: 0.7570 (mpt90) cc_final: 0.7213 (mmt180) REVERT: L 124 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: L 199 LEU cc_start: 0.8042 (tt) cc_final: 0.7668 (tm) outliers start: 21 outliers final: 15 residues processed: 88 average time/residue: 1.0816 time to fit residues: 100.4345 Evaluate side-chains 91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.162269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115362 restraints weight = 6454.813| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.03 r_work: 0.3150 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0902 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= 0.152 Angle : 0.570 7.097 8429 Z= 0.294 Chirality : 0.042 0.220 967 Planarity : 0.004 0.065 1045 Dihedral : 5.346 52.591 849 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.15 % Allowed : 24.02 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.87 (0.31), residues: 780 helix: 2.51 (0.29), residues: 346 sheet: 1.44 (0.38), residues: 197 loop : -0.96 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 139 HIS 0.003 0.001 HIS Z 155 PHE 0.020 0.002 PHE Z 335 TYR 0.011 0.001 TYR H 121 ARG 0.002 0.000 ARG Z 380 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 385) hydrogen bonds : angle 4.08875 ( 1182) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.52613 ( 8) covalent geometry : bond 0.00357 ( 6207) covalent geometry : angle 0.57007 ( 8421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6287.22 seconds wall clock time: 110 minutes 31.21 seconds (6631.21 seconds total)