Starting phenix.real_space_refine on Mon Sep 23 18:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_22325.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_22325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_22325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_22325.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgf_22325/09_2024/7jgf_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-5461/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: 7.50, per 1000 atoms: 1.68 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: 1.10 Conformation dependent library (CDL) restraints added in 1.4 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: 0.52 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: 1.14 Time building geometry restraints manager: 1.29 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: 1.540 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: 0.130 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.526 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: 0.2585 time to fit residues: 16.6837 Evaluate side-chains 41 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4489 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 : 37.84 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 fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8308 (pp) cc_final: 0.7742 (pp) REVERT: A 2154 MET cc_start: 0.1808 (mtt) cc_final: -0.0917 (mmm) REVERT: A 2198 GLN cc_start: 0.8721 (pp30) cc_final: 0.8512 (pp30) REVERT: A 2422 MET cc_start: 0.7573 (pmm) cc_final: 0.6994 (pmm) REVERT: A 2434 LYS cc_start: 0.7143 (mmtp) cc_final: 0.6665 (mmtt) REVERT: A 2465 TRP cc_start: 0.5197 (t60) cc_final: 0.3992 (t60) REVERT: A 2574 PHE cc_start: 0.5683 (t80) cc_final: 0.5436 (t80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2283 time to fit residues: 15.3291 Evaluate side-chains 46 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.0980 chunk 14 optimal weight: 0.0030 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4479 moved from start: 0.1754 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= 0.094 Angle : 0.419 5.939 6089 Z= 0.234 Chirality : 0.035 0.107 620 Planarity : 0.004 0.057 776 Dihedral : 3.602 15.289 579 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 37.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: 0.60 (0.38), residues: 524 helix: 1.33 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -0.79 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2234 HIS 0.003 0.001 HIS A2200 PHE 0.020 0.001 PHE A2078 TYR 0.007 0.001 TYR A2249 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 56 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8305 (pp) cc_final: 0.7826 (pp) REVERT: A 2465 TRP cc_start: 0.5160 (t60) cc_final: 0.4204 (t60) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2169 time to fit residues: 14.9017 Evaluate side-chains 48 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.0020 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4599 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 4541 Z= 0.121 Angle : 0.454 5.144 6089 Z= 0.252 Chirality : 0.036 0.114 620 Planarity : 0.004 0.053 776 Dihedral : 3.739 16.070 579 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 45.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.41 % Allowed : 1.01 % Favored : 98.58 % 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: 0.75 (0.38), residues: 524 helix: 1.51 (0.32), residues: 280 sheet: None (None), residues: 0 loop : -0.69 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2234 HIS 0.001 0.000 HIS A2200 PHE 0.018 0.002 PHE A2064 TYR 0.007 0.001 TYR A2083 ARG 0.011 0.001 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 56 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.644 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: 0.8366 (pp) cc_final: 0.7837 (pp) REVERT: A 2154 MET cc_start: 0.1853 (mpp) cc_final: -0.0094 (mmm) REVERT: A 2415 ARG cc_start: 0.7114 (mmt180) cc_final: 0.6814 (mmm-85) REVERT: A 2465 TRP cc_start: 0.5201 (t60) cc_final: 0.4447 (t60) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2506 time to fit residues: 17.2492 Evaluate side-chains 49 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** A2232 GLN A2503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4541 Z= 0.181 Angle : 0.616 13.376 6089 Z= 0.330 Chirality : 0.040 0.134 620 Planarity : 0.006 0.085 776 Dihedral : 4.484 21.926 579 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 56.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: 0.04 (0.37), residues: 524 helix: 1.02 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -1.16 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2511 HIS 0.003 0.001 HIS A2200 PHE 0.024 0.002 PHE A2078 TYR 0.013 0.002 TYR A2031 ARG 0.010 0.001 ARG A2127 *********************** 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 58 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8415 (pp) cc_final: 0.7880 (pp) REVERT: A 2154 MET cc_start: 0.2150 (mpp) cc_final: 0.0525 (mtp) REVERT: A 2465 TRP cc_start: 0.5481 (t60) cc_final: 0.4792 (t60) REVERT: A 2472 ILE cc_start: 0.8435 (tp) cc_final: 0.8163 (tp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2282 time to fit residues: 16.2527 Evaluate side-chains 47 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4722 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4541 Z= 0.106 Angle : 0.443 5.225 6089 Z= 0.247 Chirality : 0.036 0.112 620 Planarity : 0.004 0.048 776 Dihedral : 4.027 19.461 579 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 49.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: 0.56 (0.37), residues: 524 helix: 1.31 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.83 (0.43), 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 0.028 0.002 PHE A2078 TYR 0.007 0.001 TYR A2083 ARG 0.008 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 56 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8342 (pp) cc_final: 0.7844 (pp) REVERT: A 2154 MET cc_start: 0.2187 (mpp) cc_final: 0.0587 (mtp) REVERT: A 2465 TRP cc_start: 0.5218 (t60) cc_final: 0.4772 (t60) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2039 time to fit residues: 14.2175 Evaluate side-chains 44 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4541 Z= 0.107 Angle : 0.439 5.246 6089 Z= 0.246 Chirality : 0.036 0.111 620 Planarity : 0.004 0.049 776 Dihedral : 3.897 19.176 579 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 49.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.41 % Allowed : 1.01 % Favored : 98.58 % 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: 0.62 (0.37), residues: 524 helix: 1.32 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.76 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2234 HIS 0.001 0.000 HIS A2471 PHE 0.026 0.002 PHE A2078 TYR 0.008 0.001 TYR A2083 ARG 0.008 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 fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8362 (pp) cc_final: 0.7866 (pp) REVERT: A 2154 MET cc_start: 0.2202 (mpp) cc_final: 0.1021 (mtp) REVERT: A 2465 TRP cc_start: 0.5268 (t60) cc_final: 0.4728 (t60) REVERT: A 2472 ILE cc_start: 0.8468 (tp) cc_final: 0.8210 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2171 time to fit residues: 14.6193 Evaluate side-chains 45 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.0010 chunk 28 optimal weight: 5.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4698 moved from start: 0.3923 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= 0.101 Angle : 0.430 5.050 6089 Z= 0.241 Chirality : 0.036 0.113 620 Planarity : 0.004 0.048 776 Dihedral : 3.792 18.419 579 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 47.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.41 % Allowed : 0.41 % Favored : 99.19 % 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: 0.81 (0.38), residues: 524 helix: 1.46 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -0.64 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A2511 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.001 PHE A2078 TYR 0.007 0.001 TYR A2083 ARG 0.008 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 fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.484 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: 0.8350 (pp) cc_final: 0.7874 (pp) REVERT: A 2154 MET cc_start: 0.2262 (mpp) cc_final: 0.0989 (mtp) REVERT: A 2195 ILE cc_start: 0.7859 (mp) cc_final: 0.7557 (mp) REVERT: A 2198 GLN cc_start: 0.8743 (pp30) cc_final: 0.8538 (pp30) REVERT: A 2465 TRP cc_start: 0.5162 (t60) cc_final: 0.4756 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2102 time to fit residues: 14.2669 Evaluate side-chains 47 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4541 Z= 0.103 Angle : 0.439 5.010 6089 Z= 0.246 Chirality : 0.036 0.114 620 Planarity : 0.004 0.048 776 Dihedral : 3.744 18.063 579 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 48.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.41 % Allowed : 0.41 % Favored : 99.19 % 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: 0.86 (0.38), residues: 524 helix: 1.49 (0.31), residues: 292 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A2511 HIS 0.002 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.008 0.001 TYR A2083 ARG 0.010 0.001 ARG A2127 *********************** 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 55 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8354 (pp) cc_final: 0.7876 (pp) REVERT: A 2154 MET cc_start: 0.2274 (mpp) cc_final: 0.0995 (mtp) REVERT: A 2465 TRP cc_start: 0.5183 (t60) cc_final: 0.4818 (t60) REVERT: A 2472 ILE cc_start: 0.8548 (tp) cc_final: 0.8317 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2118 time to fit residues: 14.4648 Evaluate side-chains 47 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 12 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7476 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4541 Z= 0.108 Angle : 0.447 6.665 6089 Z= 0.249 Chirality : 0.036 0.136 620 Planarity : 0.004 0.048 776 Dihedral : 3.735 18.407 579 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 49.29 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: 0.88 (0.38), residues: 524 helix: 1.55 (0.31), residues: 288 sheet: None (None), residues: 0 loop : -0.61 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A2511 HIS 0.001 0.000 HIS A2338 PHE 0.026 0.002 PHE A2078 TYR 0.008 0.001 TYR A2083 ARG 0.010 0.001 ARG A2248 ********************** 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 56 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2093 LEU cc_start: 0.8339 (pp) cc_final: 0.7846 (pp) REVERT: A 2154 MET cc_start: 0.2408 (mpp) cc_final: 0.1013 (mtp) REVERT: A 2465 TRP cc_start: 0.5238 (t60) cc_final: 0.4897 (t60) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1982 time to fit residues: 13.8039 Evaluate side-chains 47 residues out of total 487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4801 r_free = 0.4801 target = 0.213883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.195621 restraints weight = 40705.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.200399 restraints weight = 33269.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.201976 restraints weight = 22405.913| |-----------------------------------------------------------------------------| r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4674 r_free = 0.4674 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4673 r_free = 0.4673 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4687 moved from start: 0.4209 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= 0.099 Angle : 0.444 5.938 6089 Z= 0.248 Chirality : 0.036 0.126 620 Planarity : 0.004 0.048 776 Dihedral : 3.702 17.640 579 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 47.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: 0.89 (0.38), residues: 524 helix: 1.53 (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 0.025 0.001 TRP A2511 HIS 0.001 0.000 HIS A2338 PHE 0.030 0.002 PHE A2574 TYR 0.008 0.001 TYR A2083 ARG 0.010 0.001 ARG A2127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.56 seconds wall clock time: 25 minutes 50.03 seconds (1550.03 seconds total)