Starting phenix.real_space_refine on Tue Feb 11 05:07:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.map" model { file = "/net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9w_31499/02_2025/7f9w_31499.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2654 2.51 5 N 713 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4217 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 bond proxies already assigned to first conformer: 863 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1669 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 25 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 25 " occ=0.50 Time building chain proxies: 4.00, per 1000 atoms: 0.95 Number of scatterers: 4217 At special positions: 0 Unit cell: (64.26, 64.8, 116.1, 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 22 16.00 O 828 8.00 N 713 7.00 C 2654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " 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: 0.94 Conformation dependent library (CDL) restraints added in 635.5 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.834A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.700A pdb=" N LEU C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.727A pdb=" N LYS C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.705A pdb=" N GLN A 130 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 145 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.612A pdb=" N TYR A 20 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.878A pdb=" N LEU A 45 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.136A pdb=" N LEU C 11 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 90 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 91 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 41 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.532A pdb=" N THR C 78 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.811A pdb=" N LYS C 36 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.542A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 138 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 185 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.827A pdb=" N TRP C 154 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 198 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.571A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 33 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 162 through 163 142 hydrogen bonds defined for protein. 348 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: 0.99 Time building geometry restraints manager: 1.13 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: 1349 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4322 Sorted by residual: bond pdb=" CB PRO C 147 " pdb=" CG PRO C 147 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C PHE C 104 " pdb=" N GLY C 105 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 ... (remaining 4317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 5437 1.16 - 2.33: 351 2.33 - 3.49: 68 3.49 - 4.66: 14 4.66 - 5.82: 5 Bond angle restraints: 5875 Sorted by residual: angle pdb=" C GLN C 96 " pdb=" N TYR C 97 " pdb=" CA TYR C 97 " ideal model delta sigma weight residual 122.65 116.83 5.82 1.66e+00 3.63e-01 1.23e+01 angle pdb=" N TYR C 146 " pdb=" CA TYR C 146 " pdb=" C TYR C 146 " ideal model delta sigma weight residual 108.82 103.55 5.27 1.69e+00 3.50e-01 9.74e+00 angle pdb=" C GLU A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C HIS B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta sigma weight residual 120.09 123.62 -3.53 1.25e+00 6.40e-01 7.99e+00 angle pdb=" C LEU B 133 " pdb=" N ALA B 134 " pdb=" CA ALA B 134 " ideal model delta sigma weight residual 120.60 124.34 -3.74 1.53e+00 4.27e-01 5.99e+00 ... (remaining 5870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2385 16.30 - 32.61: 150 32.61 - 48.91: 40 48.91 - 65.21: 3 65.21 - 81.52: 13 Dihedral angle restraints: 2591 sinusoidal: 1004 harmonic: 1587 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual 93.00 159.24 -66.24 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 143.75 -50.75 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.054: 182 0.054 - 0.081: 59 0.081 - 0.107: 43 0.107 - 0.134: 14 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR C 97 " pdb=" N TYR C 97 " pdb=" C TYR C 97 " pdb=" CB TYR C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 643 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 56 " -0.015 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP C 56 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 56 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 56 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 56 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 56 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 56 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 134 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 135 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 155 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 156 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 85 2.67 - 3.23: 3920 3.23 - 3.79: 6053 3.79 - 4.34: 8034 4.34 - 4.90: 13974 Nonbonded interactions: 32066 Sorted by model distance: nonbonded pdb=" OE2 GLU C 111 " pdb=" NE2 GLN C 172 " model vdw 2.114 3.120 nonbonded pdb=" OG SER B 212 " pdb=" OG1 THR B 214 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A 47 " pdb=" O SER A 54 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 83 " pdb=" NE2 GLN C 85 " model vdw 2.221 3.120 nonbonded pdb=" N GLY A 141 " pdb=" OG SER B 104 " model vdw 2.252 3.120 ... (remaining 32061 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=0.50 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.340 Process input model: 15.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.005 0.049 4322 Z= 0.334 Angle : 0.677 5.819 5875 Z= 0.371 Chirality : 0.043 0.134 646 Planarity : 0.005 0.053 753 Dihedral : 12.990 81.517 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.63 % Allowed : 0.21 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.38), residues: 539 helix: 0.20 (1.48), residues: 13 sheet: 0.41 (0.37), residues: 234 loop : 0.05 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 56 HIS 0.002 0.000 HIS B 173 PHE 0.014 0.002 PHE C 145 TYR 0.024 0.002 TYR C 97 ARG 0.004 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.464 Fit side-chains REVERT: A 18 MET cc_start: 0.8747 (mmp) cc_final: 0.8477 (mmt) REVERT: A 26 LEU cc_start: 0.6275 (tt) cc_final: 0.5996 (tt) REVERT: A 45 LEU cc_start: 0.8311 (tp) cc_final: 0.8091 (tt) REVERT: A 106 GLU cc_start: 0.8553 (pp20) cc_final: 0.8322 (pp20) REVERT: A 155 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8381 (tmt170) REVERT: A 160 GLN cc_start: 0.8279 (mm110) cc_final: 0.8026 (mm110) REVERT: C 1 ASP cc_start: 0.8395 (p0) cc_final: 0.8182 (p0) REVERT: C 128 ASP cc_start: 0.8519 (p0) cc_final: 0.8087 (p0) REVERT: C 153 GLN cc_start: 0.7248 (mp10) cc_final: 0.6837 (mp10) REVERT: B 59 ASP cc_start: 0.7667 (t0) cc_final: 0.7417 (t0) REVERT: B 73 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1965 time to fit residues: 22.7779 Evaluate side-chains 83 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN B 6 GLN B 65 GLN B 206 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089011 restraints weight = 26017.686| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 6.74 r_work: 0.3036 rms_B_bonded: 5.92 restraints_weight: 2.0000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4322 Z= 0.201 Angle : 0.628 6.566 5875 Z= 0.327 Chirality : 0.043 0.151 646 Planarity : 0.005 0.042 753 Dihedral : 4.703 22.128 589 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.63 % Allowed : 5.92 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.39), residues: 539 helix: 0.80 (1.56), residues: 13 sheet: 0.53 (0.36), residues: 247 loop : 0.29 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 56 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE B 64 TYR 0.017 0.002 TYR C 97 ARG 0.005 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.548 Fit side-chains REVERT: A 9 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 18 MET cc_start: 0.9014 (mmp) cc_final: 0.8721 (mmt) REVERT: A 126 MET cc_start: 0.8806 (ppp) cc_final: 0.8505 (ppp) REVERT: A 155 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8712 (tmt170) REVERT: A 160 GLN cc_start: 0.8501 (mm110) cc_final: 0.8103 (mm110) REVERT: C 1 ASP cc_start: 0.8726 (p0) cc_final: 0.8471 (p0) REVERT: C 17 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 176 ASP cc_start: 0.8380 (m-30) cc_final: 0.8000 (t70) REVERT: B 59 ASP cc_start: 0.7746 (t0) cc_final: 0.7499 (t0) REVERT: B 64 PHE cc_start: 0.7802 (m-10) cc_final: 0.7542 (m-10) REVERT: B 73 ASP cc_start: 0.8631 (t0) cc_final: 0.8374 (t0) REVERT: B 100 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.8446 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1744 time to fit residues: 18.6935 Evaluate side-chains 80 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 0.0170 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087307 restraints weight = 25015.343| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 6.27 r_work: 0.3002 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 4322 Z= 0.355 Angle : 0.660 7.219 5875 Z= 0.347 Chirality : 0.045 0.161 646 Planarity : 0.004 0.036 753 Dihedral : 4.735 20.676 589 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.69 % Allowed : 10.36 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.38), residues: 539 helix: 0.44 (1.51), residues: 13 sheet: 0.52 (0.36), residues: 242 loop : 0.15 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 154 HIS 0.002 0.000 HIS B 173 PHE 0.008 0.002 PHE B 155 TYR 0.031 0.002 TYR C 97 ARG 0.003 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.523 Fit side-chains REVERT: A 9 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 18 MET cc_start: 0.8976 (mmp) cc_final: 0.8670 (mmt) REVERT: A 157 THR cc_start: 0.8422 (p) cc_final: 0.8179 (p) REVERT: A 160 GLN cc_start: 0.8504 (mm110) cc_final: 0.8084 (mm110) REVERT: C 1 ASP cc_start: 0.8779 (p0) cc_final: 0.8490 (p0) REVERT: C 17 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 96 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7635 (tm-30) REVERT: C 176 ASP cc_start: 0.8514 (m-30) cc_final: 0.8177 (t70) REVERT: B 59 ASP cc_start: 0.7819 (t0) cc_final: 0.7570 (t0) REVERT: B 64 PHE cc_start: 0.7169 (m-10) cc_final: 0.6916 (m-10) REVERT: B 73 ASP cc_start: 0.8622 (t0) cc_final: 0.8372 (t0) REVERT: B 157 GLU cc_start: 0.8591 (pt0) cc_final: 0.8207 (pm20) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1758 time to fit residues: 19.1445 Evaluate side-chains 86 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.127439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088270 restraints weight = 32746.680| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 7.26 r_work: 0.3008 rms_B_bonded: 6.18 restraints_weight: 2.0000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4322 Z= 0.194 Angle : 0.588 7.750 5875 Z= 0.306 Chirality : 0.043 0.156 646 Planarity : 0.004 0.032 753 Dihedral : 4.524 22.073 589 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.69 % Allowed : 11.21 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.38), residues: 539 helix: 0.72 (1.50), residues: 13 sheet: 0.68 (0.36), residues: 234 loop : 0.09 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.001 0.000 HIS C 195 PHE 0.006 0.001 PHE C 215 TYR 0.016 0.001 TYR C 97 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.466 Fit side-chains REVERT: A 9 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 18 MET cc_start: 0.9014 (mmp) cc_final: 0.8701 (mmt) REVERT: A 160 GLN cc_start: 0.8501 (mm110) cc_final: 0.8062 (mm110) REVERT: C 1 ASP cc_start: 0.8709 (p0) cc_final: 0.8414 (p0) REVERT: C 17 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 48 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8714 (mmp) REVERT: B 59 ASP cc_start: 0.7771 (t0) cc_final: 0.7494 (t0) REVERT: B 73 ASP cc_start: 0.8627 (t0) cc_final: 0.8325 (t0) REVERT: B 157 GLU cc_start: 0.8633 (pt0) cc_final: 0.8154 (pm20) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.1668 time to fit residues: 19.2370 Evaluate side-chains 87 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN B 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.129669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091383 restraints weight = 24872.131| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 6.50 r_work: 0.3084 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4322 Z= 0.155 Angle : 0.571 7.634 5875 Z= 0.295 Chirality : 0.042 0.156 646 Planarity : 0.004 0.031 753 Dihedral : 4.289 21.921 589 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.85 % Allowed : 13.53 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.38), residues: 539 helix: 0.74 (1.43), residues: 13 sheet: 0.79 (0.36), residues: 237 loop : 0.15 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.002 0.000 HIS C 195 PHE 0.018 0.001 PHE B 64 TYR 0.012 0.001 TYR A 43 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 18 MET cc_start: 0.8958 (mmp) cc_final: 0.8675 (mmt) REVERT: A 155 ARG cc_start: 0.9019 (tmm-80) cc_final: 0.8818 (tmt170) REVERT: A 160 GLN cc_start: 0.8444 (mm110) cc_final: 0.8098 (mm110) REVERT: C 1 ASP cc_start: 0.8592 (p0) cc_final: 0.8325 (p0) REVERT: C 17 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 61 GLU cc_start: 0.8749 (tp30) cc_final: 0.8490 (tp30) REVERT: C 176 ASP cc_start: 0.8182 (m-30) cc_final: 0.7764 (t70) REVERT: B 59 ASP cc_start: 0.7744 (t0) cc_final: 0.7482 (t0) REVERT: B 73 ASP cc_start: 0.8563 (t0) cc_final: 0.8241 (t0) REVERT: B 157 GLU cc_start: 0.8582 (pt0) cc_final: 0.8092 (pm20) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1838 time to fit residues: 20.1769 Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.126033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088510 restraints weight = 24414.350| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 6.22 r_work: 0.3034 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4322 Z= 0.305 Angle : 0.606 8.299 5875 Z= 0.318 Chirality : 0.043 0.153 646 Planarity : 0.004 0.040 753 Dihedral : 4.413 19.603 589 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.11 % Allowed : 13.11 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.38), residues: 539 helix: 0.53 (1.42), residues: 13 sheet: 0.71 (0.36), residues: 243 loop : 0.19 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.023 0.002 PHE B 64 TYR 0.027 0.002 TYR C 97 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.465 Fit side-chains REVERT: A 9 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 18 MET cc_start: 0.8968 (mmp) cc_final: 0.8607 (mmt) REVERT: A 126 MET cc_start: 0.8866 (ppp) cc_final: 0.8420 (ppp) REVERT: A 155 ARG cc_start: 0.9021 (tmm-80) cc_final: 0.8611 (ptm-80) REVERT: A 160 GLN cc_start: 0.8466 (mm110) cc_final: 0.8023 (mm110) REVERT: C 1 ASP cc_start: 0.8696 (p0) cc_final: 0.8392 (p0) REVERT: C 17 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 61 GLU cc_start: 0.8801 (tp30) cc_final: 0.8568 (tp30) REVERT: C 176 ASP cc_start: 0.8345 (m-30) cc_final: 0.7953 (t70) REVERT: B 59 ASP cc_start: 0.7830 (t0) cc_final: 0.7549 (t0) REVERT: B 64 PHE cc_start: 0.6946 (m-10) cc_final: 0.6613 (m-10) REVERT: B 73 ASP cc_start: 0.8550 (t0) cc_final: 0.8265 (t0) REVERT: B 157 GLU cc_start: 0.8550 (pt0) cc_final: 0.8103 (pm20) outliers start: 8 outliers final: 2 residues processed: 91 average time/residue: 0.1907 time to fit residues: 21.2226 Evaluate side-chains 84 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.0870 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.5766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090595 restraints weight = 27311.572| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 6.70 r_work: 0.3063 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4322 Z= 0.163 Angle : 0.577 8.229 5875 Z= 0.300 Chirality : 0.042 0.147 646 Planarity : 0.004 0.041 753 Dihedral : 4.223 19.449 589 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.69 % Allowed : 13.95 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.38), residues: 539 helix: 0.62 (1.41), residues: 13 sheet: 0.72 (0.36), residues: 236 loop : 0.15 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 154 HIS 0.001 0.000 HIS C 195 PHE 0.016 0.001 PHE B 64 TYR 0.012 0.001 TYR C 97 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 18 MET cc_start: 0.8979 (mmp) cc_final: 0.8643 (mmt) REVERT: A 111 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8860 (mp0) REVERT: A 126 MET cc_start: 0.8893 (ppp) cc_final: 0.8562 (ppp) REVERT: A 144 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 155 ARG cc_start: 0.9053 (tmm-80) cc_final: 0.8806 (tmt170) REVERT: A 160 GLN cc_start: 0.8446 (mm110) cc_final: 0.8086 (mm110) REVERT: C 1 ASP cc_start: 0.8633 (p0) cc_final: 0.8350 (p0) REVERT: C 17 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 61 GLU cc_start: 0.8785 (tp30) cc_final: 0.8516 (tp30) REVERT: C 176 ASP cc_start: 0.8245 (m-30) cc_final: 0.7916 (t0) REVERT: C 217 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7066 (mtm110) REVERT: B 59 ASP cc_start: 0.7782 (t0) cc_final: 0.7513 (t0) REVERT: B 73 ASP cc_start: 0.8538 (t0) cc_final: 0.8233 (t0) REVERT: B 157 GLU cc_start: 0.8557 (pt0) cc_final: 0.8067 (pm20) outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 0.1880 time to fit residues: 20.6570 Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 4 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 overall best weight: 0.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093315 restraints weight = 23158.444| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 6.28 r_work: 0.3126 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4322 Z= 0.149 Angle : 0.563 8.371 5875 Z= 0.290 Chirality : 0.041 0.148 646 Planarity : 0.004 0.034 753 Dihedral : 3.980 18.354 589 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 13.32 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 539 helix: 0.60 (1.40), residues: 13 sheet: 0.83 (0.35), residues: 237 loop : 0.15 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 154 HIS 0.002 0.000 HIS C 195 PHE 0.029 0.001 PHE B 64 TYR 0.010 0.001 TYR C 55 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 18 MET cc_start: 0.8933 (mmp) cc_final: 0.8623 (mmt) REVERT: A 126 MET cc_start: 0.8827 (ppp) cc_final: 0.8516 (ppp) REVERT: A 144 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 155 ARG cc_start: 0.9036 (tmm-80) cc_final: 0.8800 (tmt170) REVERT: A 160 GLN cc_start: 0.8415 (mm110) cc_final: 0.8073 (mm110) REVERT: C 1 ASP cc_start: 0.8566 (p0) cc_final: 0.8326 (p0) REVERT: C 17 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 61 GLU cc_start: 0.8782 (tp30) cc_final: 0.8508 (tp30) REVERT: C 111 GLU cc_start: 0.8722 (tp30) cc_final: 0.8376 (tt0) REVERT: C 176 ASP cc_start: 0.8187 (m-30) cc_final: 0.7644 (t70) REVERT: C 217 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7168 (mtm110) REVERT: B 59 ASP cc_start: 0.7760 (t0) cc_final: 0.7479 (t0) REVERT: B 73 ASP cc_start: 0.8485 (t0) cc_final: 0.8163 (t0) REVERT: B 157 GLU cc_start: 0.8486 (pt0) cc_final: 0.8003 (pm20) REVERT: B 189 SER cc_start: 0.8808 (m) cc_final: 0.8244 (p) outliers start: 8 outliers final: 5 residues processed: 95 average time/residue: 0.1859 time to fit residues: 22.1228 Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.128805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090804 restraints weight = 20175.168| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.98 r_work: 0.3081 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4322 Z= 0.209 Angle : 0.595 8.694 5875 Z= 0.307 Chirality : 0.042 0.144 646 Planarity : 0.004 0.037 753 Dihedral : 4.055 18.957 589 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.11 % Allowed : 13.74 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.38), residues: 539 helix: 0.63 (1.39), residues: 13 sheet: 0.85 (0.36), residues: 235 loop : 0.14 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 154 HIS 0.001 0.000 HIS C 195 PHE 0.027 0.001 PHE B 64 TYR 0.018 0.001 TYR C 97 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.512 Fit side-chains REVERT: A 9 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 18 MET cc_start: 0.8961 (mmp) cc_final: 0.8608 (mmt) REVERT: A 126 MET cc_start: 0.8852 (ppp) cc_final: 0.8547 (ppp) REVERT: A 155 ARG cc_start: 0.9042 (tmm-80) cc_final: 0.8803 (tmt170) REVERT: A 157 THR cc_start: 0.8052 (p) cc_final: 0.7531 (p) REVERT: A 160 GLN cc_start: 0.8414 (mm110) cc_final: 0.8051 (mm110) REVERT: C 1 ASP cc_start: 0.8596 (p0) cc_final: 0.8320 (p0) REVERT: C 17 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8124 (tm-30) REVERT: C 111 GLU cc_start: 0.8723 (tp30) cc_final: 0.8391 (tt0) REVERT: C 176 ASP cc_start: 0.8237 (m-30) cc_final: 0.7705 (t70) REVERT: C 217 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7234 (mtm110) REVERT: B 59 ASP cc_start: 0.7816 (t0) cc_final: 0.7528 (t0) REVERT: B 73 ASP cc_start: 0.8502 (t0) cc_final: 0.8175 (t0) REVERT: B 81 MET cc_start: 0.7577 (ttt) cc_final: 0.7347 (ttt) REVERT: B 157 GLU cc_start: 0.8484 (pt0) cc_final: 0.8000 (pm20) REVERT: B 189 SER cc_start: 0.8815 (m) cc_final: 0.8289 (p) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.1689 time to fit residues: 19.1930 Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089297 restraints weight = 21989.613| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 6.16 r_work: 0.3047 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4322 Z= 0.238 Angle : 0.592 8.837 5875 Z= 0.305 Chirality : 0.042 0.148 646 Planarity : 0.004 0.035 753 Dihedral : 4.204 20.614 589 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.11 % Allowed : 13.53 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.38), residues: 539 helix: 0.60 (1.38), residues: 13 sheet: 0.78 (0.36), residues: 235 loop : 0.11 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.026 0.001 PHE B 64 TYR 0.021 0.002 TYR C 97 ARG 0.006 0.001 ARG C 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.482 Fit side-chains REVERT: A 9 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 18 MET cc_start: 0.9021 (mmp) cc_final: 0.8643 (mmt) REVERT: A 126 MET cc_start: 0.8870 (ppp) cc_final: 0.8450 (ppp) REVERT: A 144 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 155 ARG cc_start: 0.9053 (tmm-80) cc_final: 0.8809 (tmt170) REVERT: A 157 THR cc_start: 0.8104 (p) cc_final: 0.7600 (p) REVERT: A 160 GLN cc_start: 0.8435 (mm110) cc_final: 0.8067 (mm110) REVERT: C 1 ASP cc_start: 0.8619 (p0) cc_final: 0.8305 (p0) REVERT: C 17 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 61 GLU cc_start: 0.9005 (tp30) cc_final: 0.8725 (tp30) REVERT: C 111 GLU cc_start: 0.8720 (tp30) cc_final: 0.8393 (tt0) REVERT: C 176 ASP cc_start: 0.8273 (m-30) cc_final: 0.7949 (t0) REVERT: C 217 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7204 (mtm110) REVERT: B 48 MET cc_start: 0.9246 (mmt) cc_final: 0.8676 (mmt) REVERT: B 59 ASP cc_start: 0.7823 (t0) cc_final: 0.7544 (t0) REVERT: B 73 ASP cc_start: 0.8528 (t0) cc_final: 0.8198 (t0) REVERT: B 81 MET cc_start: 0.7643 (ttt) cc_final: 0.7401 (ttt) REVERT: B 157 GLU cc_start: 0.8458 (pt0) cc_final: 0.7966 (pm20) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.1799 time to fit residues: 19.6810 Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.128426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090246 restraints weight = 22451.243| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 6.17 r_work: 0.3077 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4322 Z= 0.182 Angle : 0.590 8.684 5875 Z= 0.303 Chirality : 0.042 0.149 646 Planarity : 0.004 0.034 753 Dihedral : 4.166 24.054 589 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 14.16 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.38), residues: 539 helix: 0.55 (1.33), residues: 13 sheet: 0.74 (0.35), residues: 235 loop : 0.10 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 154 HIS 0.001 0.000 HIS C 195 PHE 0.029 0.001 PHE B 64 TYR 0.014 0.001 TYR C 97 ARG 0.005 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2865.01 seconds wall clock time: 51 minutes 35.18 seconds (3095.18 seconds total)