Starting phenix.real_space_refine on Tue Feb 11 07:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.map" model { file = "/net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgf_22325/02_2025/7jgf_22325.cif" } resolution = 4.69 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= 1.000 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 2808 2.51 5 N 770 2.21 5 O 839 1.98 5 H 30 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4477 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4477 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 532, 4455 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 532, 4455 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 4528 Conformer: "C" Number of residues, atoms: 532, 4439 Classifications: {'peptide': 532} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4528 Time building chain proxies: 7.19, per 1000 atoms: 1.61 Number of scatterers: 4477 At special positions: 0 Unit cell: (74.06, 137.54, 93.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 839 8.00 N 770 7.00 C 2808 6.00 H 30 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A2208 " - pdb=" SG CYS A2224 " distance=2.03 Simple disulfide: pdb=" SG CYS A2331 " - pdb=" SG CYS A2478 " distance=2.03 Simple disulfide: pdb=" SG CYS A2516 " - pdb=" SG CYS A2599 " distance=2.03 Simple disulfide: pdb=" SG CYS A2530 " - pdb=" SG CYS A2545 " distance=2.03 Simple disulfide: pdb=" SG CYS A2592 " - pdb=" SG CYS A2597 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 65.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 2023 through 2032 Processing helix chain 'A' and resid 2060 through 2086 removed outlier: 4.283A pdb=" N LEU A2079 " --> pdb=" O GLU A2075 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A2080 " --> pdb=" O GLY A2076 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A2081 " --> pdb=" O LYS A2077 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A2084 " --> pdb=" O GLY A2080 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A2085 " --> pdb=" O ASN A2081 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A2086 " --> pdb=" O TYR A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2110 removed outlier: 3.977A pdb=" N TYR A2103 " --> pdb=" O SER A2099 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU A2104 " --> pdb=" O PHE A2100 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A2105 " --> pdb=" O TYR A2101 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A2107 " --> pdb=" O TYR A2103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A2110 " --> pdb=" O ILE A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2130 removed outlier: 3.627A pdb=" N LYS A2122 " --> pdb=" O PHE A2118 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2157 removed outlier: 3.574A pdb=" N TRP A2143 " --> pdb=" O ALA A2139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS A2148 " --> pdb=" O LYS A2144 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A2149 " --> pdb=" O THR A2145 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP A2151 " --> pdb=" O LYS A2147 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET A2154 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A2155 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS A2156 " --> pdb=" O ASN A2152 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A2157 " --> pdb=" O ALA A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2183 through 2207 Processing helix chain 'A' and resid 2221 through 2252 removed outlier: 3.599A pdb=" N ILE A2240 " --> pdb=" O ARG A2236 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A2241 " --> pdb=" O LYS A2237 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A2242 " --> pdb=" O ARG A2238 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A2243 " --> pdb=" O SER A2239 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A2244 " --> pdb=" O ILE A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2300 removed outlier: 4.137A pdb=" N PHE A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2302 through 2310 removed outlier: 3.860A pdb=" N ILE A2307 " --> pdb=" O GLN A2304 " (cutoff:3.500A) Proline residue: A2308 - end of helix Processing helix chain 'A' and resid 2328 through 2337 removed outlier: 3.849A pdb=" N LYS A2333 " --> pdb=" O TYR A2329 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A2334 " --> pdb=" O ILE A2330 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A2335 " --> pdb=" O CYS A2331 " (cutoff:3.500A) Processing helix chain 'A' and resid 2367 through 2372 removed outlier: 4.344A pdb=" N ASN A2372 " --> pdb=" O PRO A2368 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2380 No H-bonds generated for 'chain 'A' and resid 2378 through 2380' Processing helix chain 'A' and resid 2381 through 2388 removed outlier: 3.527A pdb=" N TYR A2385 " --> pdb=" O LYS A2381 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A2386 " --> pdb=" O ILE A2382 " (cutoff:3.500A) Processing helix chain 'A' and resid 2388 through 2411 removed outlier: 3.975A pdb=" N PHE A2392 " --> pdb=" O ASP A2388 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A2394 " --> pdb=" O LYS A2390 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A2408 " --> pdb=" O VAL A2404 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LYS A2409 " --> pdb=" O GLU A2405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A2410 " --> pdb=" O ARG A2406 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A2411 " --> pdb=" O LEU A2407 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2433 Processing helix chain 'A' and resid 2441 through 2451 Processing helix chain 'A' and resid 2458 through 2484 removed outlier: 3.686A pdb=" N CYS A2478 " --> pdb=" O GLU A2474 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A2484 " --> pdb=" O TYR A2480 " (cutoff:3.500A) Processing helix chain 'A' and resid 2496 through 2501 removed outlier: 3.540A pdb=" N GLU A2499 " --> pdb=" O PRO A2496 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A2501 " --> pdb=" O ILE A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2502 through 2513 Processing helix chain 'A' and resid 2515 through 2529 removed outlier: 3.726A pdb=" N TYR A2523 " --> pdb=" O ARG A2519 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A2527 " --> pdb=" O TYR A2523 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A2528 " --> pdb=" O ASP A2524 " (cutoff:3.500A) Processing helix chain 'A' and resid 2546 through 2548 No H-bonds generated for 'chain 'A' and resid 2546 through 2548' Processing helix chain 'A' and resid 2549 through 2574 removed outlier: 4.107A pdb=" N LYS A2553 " --> pdb=" O CYS A2549 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A2571 " --> pdb=" O THR A2567 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A2573 " --> pdb=" O LYS A2569 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2591 removed outlier: 3.894A pdb=" N LYS A2589 " --> pdb=" O PRO A2585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2166 through 2167 210 hydrogen bonds defined for protein. 618 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: 1.10 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 30 1.05 - 1.24: 585 1.24 - 1.43: 1336 1.43 - 1.62: 2578 1.62 - 1.81: 42 Bond restraints: 4571 Sorted by residual: bond pdb=" CA PHE A2064 " pdb=" CB PHE A2064 " ideal model delta sigma weight residual 1.529 1.550 -0.021 1.74e-02 3.30e+03 1.41e+00 bond pdb=" CG MET A2422 " pdb=" SD MET A2422 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CA PHE A2574 " pdb=" C PHE A2574 " ideal model delta sigma weight residual 1.522 1.537 -0.014 1.51e-02 4.39e+03 9.22e-01 bond pdb=" CB GLU A2202 " pdb=" CG GLU A2202 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.16e-01 bond pdb=" CA PHE A2182 " pdb=" C PHE A2182 " ideal model delta sigma weight residual 1.526 1.540 -0.015 1.75e-02 3.27e+03 6.94e-01 ... (remaining 4566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5904 1.41 - 2.83: 196 2.83 - 4.24: 30 4.24 - 5.66: 10 5.66 - 7.07: 3 Bond angle restraints: 6143 Sorted by residual: angle pdb=" C ALA A2421 " pdb=" N MET A2422 " pdb=" CA MET A2422 " ideal model delta sigma weight residual 121.14 114.07 7.07 1.75e+00 3.27e-01 1.63e+01 angle pdb=" C GLU A2063 " pdb=" N PHE A2064 " pdb=" CA PHE A2064 " ideal model delta sigma weight residual 120.72 115.30 5.42 1.67e+00 3.59e-01 1.05e+01 angle pdb=" N MET A2422 " pdb=" CA MET A2422 " pdb=" CB MET A2422 " ideal model delta sigma weight residual 110.40 115.64 -5.24 1.63e+00 3.76e-01 1.03e+01 angle pdb=" N GLY A2412 " pdb=" CA GLY A2412 " pdb=" C GLY A2412 " ideal model delta sigma weight residual 110.20 114.32 -4.12 1.32e+00 5.74e-01 9.74e+00 angle pdb=" CA MET A2422 " pdb=" CB MET A2422 " pdb=" CG MET A2422 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.83e+00 ... (remaining 6138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2550 17.85 - 35.70: 223 35.70 - 53.55: 37 53.55 - 71.39: 5 71.39 - 89.24: 3 Dihedral angle restraints: 2818 sinusoidal: 1240 harmonic: 1578 Sorted by residual: dihedral pdb=" CB CYS A2208 " pdb=" SG CYS A2208 " pdb=" SG CYS A2224 " pdb=" CB CYS A2224 " ideal model delta sinusoidal sigma weight residual -86.00 3.24 -89.24 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A2516 " pdb=" SG CYS A2516 " pdb=" SG CYS A2599 " pdb=" CB CYS A2599 " ideal model delta sinusoidal sigma weight residual -86.00 -14.43 -71.57 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS A2530 " pdb=" SG CYS A2530 " pdb=" SG CYS A2545 " pdb=" CB CYS A2545 " ideal model delta sinusoidal sigma weight residual -86.00 -53.56 -32.44 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 2815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 409 0.033 - 0.065: 153 0.065 - 0.097: 43 0.097 - 0.130: 12 0.130 - 0.162: 3 Chirality restraints: 620 Sorted by residual: chirality pdb=" CA PHE A2064 " pdb=" N PHE A2064 " pdb=" C PHE A2064 " pdb=" CB PHE A2064 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CG LEU A2113 " pdb=" CB LEU A2113 " pdb=" CD1 LEU A2113 " pdb=" CD2 LEU A2113 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CB VAL A2404 " pdb=" CA VAL A2404 " pdb=" CG1 VAL A2404 " pdb=" CG2 VAL A2404 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 617 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2234 " 0.022 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP A2234 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A2234 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A2234 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2234 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A2234 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A2234 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2234 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2234 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A2234 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2495 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A2496 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A2496 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2496 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A2584 " -0.039 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A2585 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A2585 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2585 " -0.034 5.00e-02 4.00e+02 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.61: 64 2.61 - 3.11: 3665 3.11 - 3.60: 5373 3.60 - 4.10: 6676 4.10 - 4.60: 10272 Nonbonded interactions: 26050 Sorted by model distance: nonbonded pdb=" O ILE A2396 " pdb=" OG SER A2399 " model vdw 2.109 2.800 nonbonded pdb=" O TRP A2142 " pdb="HD21 ASN A2146 " model vdw 2.212 2.450 nonbonded pdb=" O ARG A2241 " pdb=" OG1 THR A2244 " model vdw 2.233 2.800 nonbonded pdb=" O MET A2467 " pdb=" ND1 HIS A2471 " model vdw 2.255 2.950 nonbonded pdb=" O GLY A2071 " pdb=" OG SER A2074 " model vdw 2.273 2.800 ... (remaining 26045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.820 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: 0.110 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4393 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 : 0.002 0.030 4541 Z= 0.154 Angle : 0.619 7.070 6089 Z= 0.364 Chirality : 0.039 0.162 620 Planarity : 0.005 0.069 776 Dihedral : 13.157 75.227 1767 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.33), residues: 524 helix: 0.10 (0.29), residues: 267 sheet: None (None), residues: 0 loop : -1.28 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A2234 HIS 0.004 0.001 HIS A2200 PHE 0.037 0.002 PHE A2078 TYR 0.018 0.001 TYR A2424 ARG 0.007 0.000 ARG A2506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8396 (pp) cc_final: 0.7924 (pp) REVERT: A 2154 MET cc_start: 0.1921 (mtt) cc_final: -0.0988 (mmm) REVERT: A 2422 MET cc_start: 0.7409 (pmm) cc_final: 0.7105 (pmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2563 time to fit residues: 16.5850 Evaluate side-chains 41 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.224218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.203916 restraints weight = 41834.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.207771 restraints weight = 34659.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.209685 restraints weight = 25910.435| |-----------------------------------------------------------------------------| r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4742 r_free = 0.4742 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4741 r_free = 0.4741 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4502 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 4541 Z= 0.138 Angle : 0.462 5.486 6089 Z= 0.261 Chirality : 0.036 0.122 620 Planarity : 0.004 0.061 776 Dihedral : 3.798 15.277 579 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 37.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.37), residues: 524 helix: 0.96 (0.31), residues: 283 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2234 HIS 0.001 0.000 HIS A2200 PHE 0.017 0.002 PHE A2078 TYR 0.011 0.001 TYR A2249 ARG 0.005 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8042 (pp) cc_final: 0.7447 (pp) REVERT: A 2154 MET cc_start: 0.1833 (mtt) cc_final: -0.1030 (mmm) REVERT: A 2422 MET cc_start: 0.7621 (pmm) cc_final: 0.7040 (pmm) REVERT: A 2434 LYS cc_start: 0.7431 (mmtp) cc_final: 0.6881 (mmtt) REVERT: A 2465 TRP cc_start: 0.5656 (t60) cc_final: 0.4297 (t60) REVERT: A 2574 PHE cc_start: 0.6244 (t80) cc_final: 0.5824 (t80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2266 time to fit residues: 15.2443 Evaluate side-chains 46 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 chunk 30 optimal weight: 0.0270 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.224674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.201542 restraints weight = 56274.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.207067 restraints weight = 42107.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.208970 restraints weight = 30560.800| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4723 r_free = 0.4723 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4479 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4541 Z= 0.094 Angle : 0.424 7.060 6089 Z= 0.234 Chirality : 0.035 0.111 620 Planarity : 0.004 0.056 776 Dihedral : 3.581 15.305 579 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 37.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.41 % Allowed : 1.42 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 524 helix: 1.36 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -0.77 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A2234 HIS 0.003 0.001 HIS A2200 PHE 0.022 0.001 PHE A2078 TYR 0.007 0.001 TYR A2103 ARG 0.006 0.000 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.7986 (pp) cc_final: 0.7526 (pp) REVERT: A 2434 LYS cc_start: 0.7245 (mmtp) cc_final: 0.6838 (mmtt) REVERT: A 2465 TRP cc_start: 0.5710 (t60) cc_final: 0.4546 (t60) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2361 time to fit residues: 15.9696 Evaluate side-chains 47 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.223092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.201475 restraints weight = 61048.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.205225 restraints weight = 46753.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.206972 restraints weight = 35724.765| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4697 r_free = 0.4697 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4697 r_free = 0.4697 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4562 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4541 Z= 0.094 Angle : 0.404 4.556 6089 Z= 0.225 Chirality : 0.035 0.107 620 Planarity : 0.004 0.053 776 Dihedral : 3.519 15.052 579 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 41.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.39), residues: 524 helix: 1.62 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.001 0.000 HIS A2086 PHE 0.017 0.001 PHE A2078 TYR 0.005 0.001 TYR A2249 ARG 0.009 0.000 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8168 (pp) cc_final: 0.7706 (pp) REVERT: A 2154 MET cc_start: 0.1977 (mpp) cc_final: -0.0224 (mmm) REVERT: A 2303 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7380 (mm-30) REVERT: A 2465 TRP cc_start: 0.5754 (t60) cc_final: 0.4515 (t60) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2206 time to fit residues: 15.4341 Evaluate side-chains 49 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.208588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.189831 restraints weight = 54753.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.194712 restraints weight = 40750.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.196601 restraints weight = 27534.104| |-----------------------------------------------------------------------------| r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4614 r_free = 0.4614 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4614 r_free = 0.4614 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4891 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4541 Z= 0.245 Angle : 0.719 9.308 6089 Z= 0.398 Chirality : 0.043 0.163 620 Planarity : 0.006 0.050 776 Dihedral : 5.123 23.346 579 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 64.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.41 % Allowed : 1.62 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.36), residues: 524 helix: 0.69 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2511 HIS 0.005 0.001 HIS A2200 PHE 0.031 0.003 PHE A2064 TYR 0.017 0.002 TYR A2103 ARG 0.019 0.002 ARG A2248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8242 (pp) cc_final: 0.7561 (pp) REVERT: A 2154 MET cc_start: 0.2936 (mpp) cc_final: 0.1127 (mtp) REVERT: A 2465 TRP cc_start: 0.5735 (t60) cc_final: 0.4657 (t60) REVERT: A 2472 ILE cc_start: 0.8445 (tp) cc_final: 0.8077 (tp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2207 time to fit residues: 16.0534 Evaluate side-chains 44 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 46 optimal weight: 0.0270 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.213266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.193059 restraints weight = 62248.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.198139 restraints weight = 45590.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.201278 restraints weight = 30418.689| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4656 r_free = 0.4656 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4744 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4541 Z= 0.113 Angle : 0.482 8.086 6089 Z= 0.264 Chirality : 0.037 0.124 620 Planarity : 0.004 0.048 776 Dihedral : 4.234 19.527 579 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 49.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 0.61 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.37), residues: 524 helix: 1.00 (0.30), residues: 286 sheet: None (None), residues: 0 loop : -0.89 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.001 0.000 HIS A2200 PHE 0.029 0.002 PHE A2078 TYR 0.013 0.001 TYR A2411 ARG 0.007 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8133 (pp) cc_final: 0.7584 (pp) REVERT: A 2154 MET cc_start: 0.2325 (mpp) cc_final: 0.0541 (mtp) REVERT: A 2406 ARG cc_start: 0.4338 (tpt90) cc_final: 0.3488 (tpt170) REVERT: A 2465 TRP cc_start: 0.5847 (t60) cc_final: 0.5050 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2234 time to fit residues: 14.9037 Evaluate side-chains 46 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.0050 chunk 26 optimal weight: 0.0070 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.213209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.195352 restraints weight = 42831.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.199570 restraints weight = 33160.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.201026 restraints weight = 24519.885| |-----------------------------------------------------------------------------| r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4740 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4541 Z= 0.104 Angle : 0.443 5.054 6089 Z= 0.246 Chirality : 0.036 0.112 620 Planarity : 0.004 0.048 776 Dihedral : 3.957 19.559 579 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 49.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.41 % Allowed : 0.81 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.38), residues: 524 helix: 1.28 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.72 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.001 0.000 HIS A2200 PHE 0.025 0.002 PHE A2078 TYR 0.012 0.001 TYR A2411 ARG 0.009 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8176 (pp) cc_final: 0.7635 (pp) REVERT: A 2154 MET cc_start: 0.2583 (mpp) cc_final: 0.0729 (mtp) REVERT: A 2465 TRP cc_start: 0.5553 (t60) cc_final: 0.4796 (t60) REVERT: A 2472 ILE cc_start: 0.8488 (tp) cc_final: 0.8112 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2128 time to fit residues: 14.3450 Evaluate side-chains 43 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.213714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.194116 restraints weight = 57503.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.199648 restraints weight = 42426.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.202109 restraints weight = 27627.389| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4651 r_free = 0.4651 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4651 r_free = 0.4651 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4736 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4541 Z= 0.105 Angle : 0.441 5.075 6089 Z= 0.247 Chirality : 0.036 0.112 620 Planarity : 0.004 0.048 776 Dihedral : 3.880 19.436 579 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 49.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.41 % Allowed : 0.81 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.38), residues: 524 helix: 1.36 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.70 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2234 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.019 0.001 TYR A2470 ARG 0.010 0.001 ARG A2127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8217 (pp) cc_final: 0.7694 (pp) REVERT: A 2154 MET cc_start: 0.2609 (mpp) cc_final: 0.1195 (mtp) REVERT: A 2472 ILE cc_start: 0.8271 (tp) cc_final: 0.7788 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2121 time to fit residues: 14.2291 Evaluate side-chains 43 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.214008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.192141 restraints weight = 73622.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.198659 restraints weight = 53795.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.201154 restraints weight = 33420.763| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4636 r_free = 0.4636 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4636 r_free = 0.4636 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 4541 Z= 0.096 Angle : 0.441 6.847 6089 Z= 0.244 Chirality : 0.036 0.127 620 Planarity : 0.004 0.047 776 Dihedral : 3.742 18.173 579 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 46.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.38), residues: 524 helix: 1.45 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.61 (0.45), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.014 0.001 TYR A2470 ARG 0.009 0.001 ARG A2248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8150 (pp) cc_final: 0.7683 (pp) REVERT: A 2154 MET cc_start: 0.2514 (mpp) cc_final: 0.1070 (mtp) REVERT: A 2195 ILE cc_start: 0.7803 (mp) cc_final: 0.7458 (mp) REVERT: A 2461 ARG cc_start: 0.6462 (ttt180) cc_final: 0.5611 (mtp180) REVERT: A 2472 ILE cc_start: 0.8307 (tp) cc_final: 0.7924 (tp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2020 time to fit residues: 13.0638 Evaluate side-chains 40 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.0770 chunk 18 optimal weight: 0.0000 chunk 10 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.216898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.197399 restraints weight = 50212.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.202803 restraints weight = 39636.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.204092 restraints weight = 26551.399| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4698 r_free = 0.4698 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4698 r_free = 0.4698 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4718 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.027 4541 Z= 0.097 Angle : 0.432 5.363 6089 Z= 0.240 Chirality : 0.036 0.120 620 Planarity : 0.004 0.047 776 Dihedral : 3.680 17.271 579 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 46.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.38), residues: 524 helix: 1.58 (0.31), residues: 288 sheet: None (None), residues: 0 loop : -0.57 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2234 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.013 0.001 TYR A2470 ARG 0.009 0.001 ARG A2127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8089 (pp) cc_final: 0.7565 (pp) REVERT: A 2127 ARG cc_start: 0.7083 (ptt180) cc_final: 0.6703 (ptt180) REVERT: A 2154 MET cc_start: 0.2528 (mpp) cc_final: 0.1014 (mtp) REVERT: A 2461 ARG cc_start: 0.6442 (ttt180) cc_final: 0.5587 (mtp180) REVERT: A 2472 ILE cc_start: 0.8285 (tp) cc_final: 0.7881 (tp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2022 time to fit residues: 13.5654 Evaluate side-chains 41 residues out of total 487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 37 optimal weight: 0.0270 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 46 optimal weight: 0.0040 chunk 47 optimal weight: 0.0020 overall best weight: 0.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.218736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.199532 restraints weight = 60251.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.204805 restraints weight = 41549.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.206812 restraints weight = 27615.417| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4713 r_free = 0.4713 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4713 r_free = 0.4713 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4644 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.028 4541 Z= 0.091 Angle : 0.423 6.213 6089 Z= 0.233 Chirality : 0.036 0.120 620 Planarity : 0.004 0.047 776 Dihedral : 3.543 15.602 579 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 44.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.41 % Allowed : 0.20 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.38), residues: 524 helix: 1.65 (0.31), residues: 288 sheet: None (None), residues: 0 loop : -0.62 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2234 HIS 0.001 0.000 HIS A2338 PHE 0.024 0.001 PHE A2078 TYR 0.013 0.001 TYR A2470 ARG 0.008 0.000 ARG A2248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.70 seconds wall clock time: 33 minutes 7.37 seconds (1987.37 seconds total)