Starting phenix.real_space_refine on Thu Mar 6 00:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9w_31499/03_2025/7f9w_31499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9w_31499/03_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_31499/03_2025/7f9w_31499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2025/7f9w_31499.map" model { file = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_2025/7f9w_31499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9w_31499/03_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-5624/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: 3.75, per 1000 atoms: 0.89 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: 0.88 Conformation dependent library (CDL) restraints added in 553.5 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: 0.58 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: 1.03 Time building geometry restraints manager: 1.08 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: 3.290 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- 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 : 0.568 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: 0.1962 time to fit residues: 22.7404 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 : 0.499 ------------------------------------------------------------------------------- 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 = 0.128075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089011 restraints weight = 26017.115| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 6.74 r_work: 0.3036 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 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 = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 6.567 5875 Z= 0.327 Chirality : 0.043 0.151 646 Planarity : 0.005 0.042 753 Dihedral : 4.703 22.127 589 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 : 0.449 Fit side-chains REVERT: A 9 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 18 MET cc_start: 0.9012 (mmp) cc_final: 0.8719 (mmt) REVERT: A 126 MET cc_start: 0.8805 (ppp) cc_final: 0.8503 (ppp) REVERT: A 155 ARG cc_start: 0.9024 (ptm-80) cc_final: 0.8708 (tmt170) REVERT: A 160 GLN cc_start: 0.8504 (mm110) cc_final: 0.8105 (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: 0.7751 (t0) cc_final: 0.7502 (t0) REVERT: B 64 PHE cc_start: 0.7800 (m-10) cc_final: 0.7540 (m-10) REVERT: B 73 ASP cc_start: 0.8629 (t0) cc_final: 0.8373 (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: 0.1677 time to fit residues: 17.9733 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 : 0.438 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.0060 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089334 restraints weight = 24172.384| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 6.25 r_work: 0.3046 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 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 = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4322 Z= 0.249 Angle : 0.617 6.988 5875 Z= 0.323 Chirality : 0.043 0.160 646 Planarity : 0.004 0.035 753 Dihedral : 4.550 20.974 589 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 10.15 % Favored : 88.16 % 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: 0.53 (0.38), residues: 539 helix: 0.65 (1.56), residues: 13 sheet: 0.60 (0.35), residues: 244 loop : 0.24 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.008 0.001 PHE B 64 TYR 0.022 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 : 0.830 Fit side-chains REVERT: A 9 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 18 MET cc_start: 0.8956 (mmp) cc_final: 0.8679 (mmt) REVERT: A 157 THR cc_start: 0.8384 (p) cc_final: 0.8100 (p) REVERT: A 160 GLN cc_start: 0.8487 (mm110) cc_final: 0.8094 (mm110) REVERT: C 1 ASP cc_start: 0.8734 (p0) cc_final: 0.8467 (p0) REVERT: C 17 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 176 ASP cc_start: 0.8454 (m-30) cc_final: 0.8097 (t70) REVERT: B 59 ASP cc_start: 0.7794 (t0) cc_final: 0.7555 (t0) REVERT: B 73 ASP cc_start: 0.8626 (t0) cc_final: 0.8363 (t0) REVERT: B 157 GLU cc_start: 0.8548 (pt0) cc_final: 0.8151 (pm20) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1709 time to fit residues: 19.0362 Evaluate side-chains 82 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 3.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** B 208 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 = 0.3814 r_free = 0.3814 target = 0.125395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.085533 restraints weight = 33630.824| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 7.29 r_work: 0.2957 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 4322 Z= 0.353 Angle : 0.656 7.955 5875 Z= 0.342 Chirality : 0.045 0.163 646 Planarity : 0.004 0.035 753 Dihedral : 4.699 21.651 589 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.69 % Allowed : 12.26 % Favored : 86.05 % 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: 0.38 (0.38), residues: 539 helix: 0.49 (1.50), residues: 13 sheet: 0.51 (0.36), residues: 242 loop : 0.13 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 154 HIS 0.002 0.000 HIS B 173 PHE 0.008 0.001 PHE C 77 TYR 0.030 0.002 TYR C 97 ARG 0.004 0.001 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 93 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.445 Fit side-chains REVERT: A 9 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 18 MET cc_start: 0.9016 (mmp) cc_final: 0.8669 (mmt) REVERT: A 155 ARG cc_start: 0.8298 (ptm-80) cc_final: 0.7995 (tmt170) REVERT: A 157 THR cc_start: 0.8342 (p) cc_final: 0.8059 (p) REVERT: A 160 GLN cc_start: 0.8526 (mm110) cc_final: 0.8086 (mm110) REVERT: C 1 ASP cc_start: 0.8757 (p0) cc_final: 0.8429 (p0) REVERT: C 17 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 59 ASP cc_start: 0.7845 (t0) cc_final: 0.7578 (t0) REVERT: B 73 ASP cc_start: 0.8636 (t0) cc_final: 0.8335 (t0) REVERT: B 157 GLU cc_start: 0.8637 (pt0) cc_final: 0.8190 (pm20) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.1961 time to fit residues: 21.6565 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER 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: 2.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.126922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.088535 restraints weight = 25141.012| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 6.44 r_work: 0.3016 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 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 = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2116 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= 0.218 Angle : 0.610 8.226 5875 Z= 0.314 Chirality : 0.043 0.153 646 Planarity : 0.004 0.036 753 Dihedral : 4.526 21.855 589 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.11 % Allowed : 12.68 % Favored : 85.20 % 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: 0.51 (0.38), residues: 539 helix: 0.56 (1.48), residues: 13 sheet: 0.64 (0.35), residues: 245 loop : 0.17 (0.39), residues: 281 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 0.009 0.001 PHE B 64 TYR 0.017 0.001 TYR C 97 ARG 0.005 0.001 ARG C 217 *********************** 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 96 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.445 Fit side-chains REVERT: A 9 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 18 MET cc_start: 0.8983 (mmp) cc_final: 0.8650 (mmt) REVERT: A 126 MET cc_start: 0.8804 (ppp) cc_final: 0.8437 (ppp) REVERT: A 144 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 160 GLN cc_start: 0.8503 (mm110) cc_final: 0.8059 (mm110) REVERT: C 1 ASP cc_start: 0.8684 (p0) cc_final: 0.8375 (p0) REVERT: C 17 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 176 ASP cc_start: 0.8326 (m-30) cc_final: 0.7956 (t70) REVERT: B 48 MET cc_start: 0.9037 (mmp) cc_final: 0.8741 (mmt) REVERT: B 59 ASP cc_start: 0.7803 (t0) cc_final: 0.7542 (t0) REVERT: B 73 ASP cc_start: 0.8614 (t0) cc_final: 0.8318 (t0) REVERT: B 157 GLU cc_start: 0.8593 (pt0) cc_final: 0.8112 (pm20) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 0.1734 time to fit residues: 19.5223 Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.0270 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.125577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087835 restraints weight = 24088.787| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 6.27 r_work: 0.3017 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 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 = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4322 Z= 0.252 Angle : 0.607 8.197 5875 Z= 0.316 Chirality : 0.043 0.150 646 Planarity : 0.004 0.038 753 Dihedral : 4.447 20.926 589 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.33 % Allowed : 12.68 % Favored : 84.99 % 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: 0.43 (0.38), residues: 539 helix: 0.55 (1.45), residues: 13 sheet: 0.69 (0.36), residues: 233 loop : 0.02 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.007 0.001 PHE B 64 TYR 0.022 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 97 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.479 Fit side-chains REVERT: A 9 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 18 MET cc_start: 0.8985 (mmp) cc_final: 0.8628 (mmt) REVERT: A 111 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8895 (mp0) REVERT: A 126 MET cc_start: 0.8833 (ppp) cc_final: 0.8532 (ppp) REVERT: A 160 GLN cc_start: 0.8471 (mm110) cc_final: 0.8036 (mm110) REVERT: C 1 ASP cc_start: 0.8682 (p0) cc_final: 0.8364 (p0) REVERT: C 17 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 176 ASP cc_start: 0.8342 (m-30) cc_final: 0.7993 (t70) REVERT: C 217 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7093 (mtm110) REVERT: B 59 ASP cc_start: 0.7866 (t0) cc_final: 0.7597 (t0) REVERT: B 73 ASP cc_start: 0.8575 (t0) cc_final: 0.8293 (t0) REVERT: B 157 GLU cc_start: 0.8558 (pt0) cc_final: 0.8095 (pm20) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 0.1781 time to fit residues: 20.6739 Evaluate side-chains 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER 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: 0.0070 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.3810 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.128787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.090896 restraints weight = 27240.234| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 6.69 r_work: 0.3063 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 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 = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2471 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= 0.158 Angle : 0.586 8.150 5875 Z= 0.303 Chirality : 0.042 0.150 646 Planarity : 0.004 0.031 753 Dihedral : 4.255 20.881 589 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.48 % Allowed : 14.59 % Favored : 83.93 % 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: 0.57 (0.38), residues: 539 helix: 0.68 (1.43), residues: 13 sheet: 0.77 (0.36), residues: 237 loop : 0.12 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 154 HIS 0.002 0.000 HIS C 195 PHE 0.006 0.001 PHE A 121 TYR 0.012 0.001 TYR A 43 ARG 0.005 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: 5 poor density : 86 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 18 MET cc_start: 0.8992 (mmp) cc_final: 0.8659 (mmt) REVERT: A 111 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8805 (mp0) REVERT: A 126 MET cc_start: 0.8825 (ppp) cc_final: 0.8489 (ppp) REVERT: A 144 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 160 GLN cc_start: 0.8484 (mm110) cc_final: 0.8053 (mm110) REVERT: C 1 ASP cc_start: 0.8622 (p0) cc_final: 0.8331 (p0) REVERT: C 17 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 111 GLU cc_start: 0.8671 (tp30) cc_final: 0.8293 (tt0) REVERT: C 176 ASP cc_start: 0.8242 (m-30) cc_final: 0.7896 (t0) REVERT: C 217 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7148 (mtm110) REVERT: B 59 ASP cc_start: 0.7837 (t0) cc_final: 0.7559 (t0) REVERT: B 73 ASP cc_start: 0.8536 (t0) cc_final: 0.8239 (t0) REVERT: B 157 GLU cc_start: 0.8548 (pt0) cc_final: 0.8064 (pm20) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1605 time to fit residues: 18.1688 Evaluate side-chains 85 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 SER 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: 2.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.0970 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.128003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090673 restraints weight = 23473.879| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 6.18 r_work: 0.3068 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 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 = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4322 Z= 0.199 Angle : 0.606 8.530 5875 Z= 0.312 Chirality : 0.042 0.147 646 Planarity : 0.004 0.041 753 Dihedral : 4.215 19.941 589 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.90 % Allowed : 13.74 % 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: 0.53 (0.38), residues: 539 helix: 0.68 (1.41), residues: 13 sheet: 0.79 (0.36), residues: 235 loop : 0.05 (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 0.006 0.001 PHE C 215 TYR 0.016 0.001 TYR C 97 ARG 0.005 0.000 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 92 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.454 Fit side-chains REVERT: A 9 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 18 MET cc_start: 0.8968 (mmp) cc_final: 0.8629 (mmt) REVERT: A 126 MET cc_start: 0.8804 (ppp) cc_final: 0.8519 (ppp) REVERT: A 160 GLN cc_start: 0.8443 (mm110) cc_final: 0.8059 (mm110) REVERT: C 1 ASP cc_start: 0.8635 (p0) cc_final: 0.8345 (p0) REVERT: C 17 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 111 GLU cc_start: 0.8672 (tp30) cc_final: 0.8290 (tt0) REVERT: C 176 ASP cc_start: 0.8273 (m-30) cc_final: 0.7944 (t0) REVERT: C 217 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7193 (mtm110) REVERT: B 59 ASP cc_start: 0.7878 (t0) cc_final: 0.7612 (t0) REVERT: B 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8204 (t0) REVERT: B 157 GLU cc_start: 0.8515 (pt0) cc_final: 0.8034 (pm20) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1643 time to fit residues: 18.6260 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.0470 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.128920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.091598 restraints weight = 20181.784| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 5.88 r_work: 0.3087 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 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 = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4322 Z= 0.171 Angle : 0.590 8.644 5875 Z= 0.303 Chirality : 0.042 0.145 646 Planarity : 0.004 0.037 753 Dihedral : 4.163 18.658 589 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 15.22 % Favored : 83.09 % 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: 0.73 (1.38), residues: 13 sheet: 0.76 (0.36), residues: 235 loop : 0.07 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 156 HIS 0.002 0.000 HIS C 195 PHE 0.006 0.001 PHE C 215 TYR 0.013 0.001 TYR C 97 ARG 0.005 0.000 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 90 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.451 Fit side-chains REVERT: A 9 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 18 MET cc_start: 0.8993 (mmp) cc_final: 0.8644 (mmt) REVERT: A 126 MET cc_start: 0.8799 (ppp) cc_final: 0.8478 (ppp) REVERT: A 160 GLN cc_start: 0.8447 (mm110) cc_final: 0.8075 (mm110) REVERT: C 1 ASP cc_start: 0.8591 (p0) cc_final: 0.8308 (p0) REVERT: C 17 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 111 GLU cc_start: 0.8634 (tp30) cc_final: 0.8269 (tt0) REVERT: C 129 GLU cc_start: 0.8698 (mp0) cc_final: 0.8477 (mp0) REVERT: C 176 ASP cc_start: 0.8227 (m-30) cc_final: 0.7900 (t0) REVERT: C 217 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7281 (mtm110) REVERT: B 59 ASP cc_start: 0.7867 (t0) cc_final: 0.7596 (t0) REVERT: B 73 ASP cc_start: 0.8497 (t0) cc_final: 0.8185 (t0) REVERT: B 157 GLU cc_start: 0.8492 (pt0) cc_final: 0.8002 (pm20) outliers start: 6 outliers final: 6 residues processed: 88 average time/residue: 0.1644 time to fit residues: 18.1295 Evaluate side-chains 89 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 0.0470 chunk 48 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088587 restraints weight = 23076.490| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 6.16 r_work: 0.3033 rms_B_bonded: 5.48 restraints_weight: 2.0000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 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 = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4322 Z= 0.269 Angle : 0.633 8.994 5875 Z= 0.328 Chirality : 0.043 0.150 646 Planarity : 0.004 0.036 753 Dihedral : 4.312 19.472 589 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.33 % Allowed : 14.59 % Favored : 83.09 % 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: 0.49 (0.38), residues: 539 helix: 0.62 (1.38), residues: 13 sheet: 0.62 (0.36), residues: 243 loop : 0.16 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.006 0.001 PHE C 215 TYR 0.023 0.002 TYR C 97 ARG 0.005 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 95 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.745 Fit side-chains REVERT: A 9 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7646 (tm-30) REVERT: A 18 MET cc_start: 0.9022 (mmp) cc_final: 0.8634 (mmt) REVERT: A 126 MET cc_start: 0.8821 (ppp) cc_final: 0.8534 (ppp) REVERT: A 155 ARG cc_start: 0.8190 (tmt170) cc_final: 0.7972 (ttp80) REVERT: A 160 GLN cc_start: 0.8478 (mm110) cc_final: 0.8096 (mm110) REVERT: C 1 ASP cc_start: 0.8650 (p0) cc_final: 0.8330 (p0) REVERT: C 17 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 111 GLU cc_start: 0.8658 (tp30) cc_final: 0.8278 (tt0) REVERT: C 129 GLU cc_start: 0.8662 (mp0) cc_final: 0.8445 (mp0) REVERT: C 176 ASP cc_start: 0.8329 (m-30) cc_final: 0.8025 (t0) REVERT: C 217 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7270 (mtm110) REVERT: B 59 ASP cc_start: 0.7902 (t0) cc_final: 0.7637 (t0) REVERT: B 73 ASP cc_start: 0.8523 (t0) cc_final: 0.8210 (t0) REVERT: B 157 GLU cc_start: 0.8511 (pt0) cc_final: 0.8028 (pm20) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.3226 time to fit residues: 38.1734 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 : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL 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: 3.9990 chunk 16 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090217 restraints weight = 22744.385| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 6.18 r_work: 0.3055 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2610 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= 0.202 Angle : 0.630 8.856 5875 Z= 0.319 Chirality : 0.042 0.148 646 Planarity : 0.004 0.033 753 Dihedral : 4.308 20.852 589 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 15.22 % Favored : 82.45 % 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: 0.45 (0.38), residues: 539 helix: 0.64 (1.36), residues: 13 sheet: 0.68 (0.36), residues: 235 loop : 0.05 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.005 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.41 seconds wall clock time: 58 minutes 2.14 seconds (3482.14 seconds total)