Starting phenix.real_space_refine on Wed Jan 17 18:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/01_2024/8d9k_27264.pdb" } resolution = 3.72 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= 0.006 sd= 0.030 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 P 65 5.49 5 S 21 5.16 5 C 3387 2.51 5 N 993 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1740 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 15, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2578 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321} Chain breaks: 3 Chain: "C" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1390 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 29} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" N TYR A 37 " occ=0.88 ... (10 atoms not shown) pdb=" OH TYR A 37 " occ=0.88 residue: pdb=" N GLU A 43 " occ=0.83 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.83 residue: pdb=" N ASP A 45 " occ=0.96 ... (6 atoms not shown) pdb=" OD2 ASP A 45 " occ=0.96 residue: pdb=" N TYR A 50 " occ=0.90 ... (10 atoms not shown) pdb=" OH TYR A 50 " occ=0.90 residue: pdb=" N GLU A 52 " occ=0.87 ... (7 atoms not shown) pdb=" OE2 GLU A 52 " occ=0.87 residue: pdb=" N PHE A 53 " occ=0.93 ... (9 atoms not shown) pdb=" CZ PHE A 53 " occ=0.93 residue: pdb=" N PHE A 54 " occ=0.88 ... (9 atoms not shown) pdb=" CZ PHE A 54 " occ=0.88 residue: pdb=" N GLU A 79 " occ=0.85 ... (7 atoms not shown) pdb=" OE2 GLU A 79 " occ=0.85 residue: pdb=" N LYS A 111 " occ=0.98 ... (7 atoms not shown) pdb=" NZ LYS A 111 " occ=0.98 residue: pdb=" N ARG A 121 " occ=0.88 ... (9 atoms not shown) pdb=" NH2 ARG A 121 " occ=0.88 residue: pdb=" N ARG A 138 " occ=0.99 ... (9 atoms not shown) pdb=" NH2 ARG A 138 " occ=0.99 residue: pdb=" N MET A 142 " occ=0.86 ... (6 atoms not shown) pdb=" CE MET A 142 " occ=0.86 ... (remaining 31 not shown) Time building chain proxies: 3.95, per 1000 atoms: 0.69 Number of scatterers: 5708 At special positions: 0 Unit cell: (64.74, 100.845, 110.805, 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 21 16.00 P 65 15.00 O 1242 8.00 N 993 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.61 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 8 sheets defined 22.7% alpha, 31.9% beta 27 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.844A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.629A pdb=" N ALA A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 221 through 226 removed outlier: 4.069A pdb=" N SER A 226 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.728A pdb=" N HIS A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.604A pdb=" N GLN B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 343 through 348 removed outlier: 4.398A pdb=" N LEU B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.975A pdb=" N SER B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 5.498A pdb=" N VAL A 78 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU A 104 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 80 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU A 106 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP A 82 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU A 79 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N MET A 157 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 81 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE A 159 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 83 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 192 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69 removed outlier: 6.463A pdb=" N LEU B 85 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 98 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 87 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.655A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 126 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.951A pdb=" N ASP B 150 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 169 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 180 " --> pdb=" O TRP B 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.854A pdb=" N ARG B 193 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 213 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS B 226 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 215 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.836A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B 282 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP B 274 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU B 280 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 298 removed outlier: 3.981A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1574 1.34 - 1.45: 1394 1.45 - 1.57: 2850 1.57 - 1.69: 128 1.69 - 1.81: 27 Bond restraints: 5973 Sorted by residual: bond pdb=" CG PRO B 92 " pdb=" CD PRO B 92 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.36e-01 bond pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta sigma weight residual 1.462 1.472 -0.010 1.54e-02 4.22e+03 4.02e-01 bond pdb=" CA PHE A 166 " pdb=" CB PHE A 166 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.54e-02 4.22e+03 3.50e-01 bond pdb=" N GLU B 114 " pdb=" CA GLU B 114 " ideal model delta sigma weight residual 1.461 1.470 -0.009 1.52e-02 4.33e+03 3.14e-01 bond pdb=" CA GLU B 167 " pdb=" CB GLU B 167 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.69e-02 3.50e+03 2.79e-01 ... (remaining 5968 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 535 107.39 - 114.04: 3467 114.04 - 120.69: 2306 120.69 - 127.34: 1927 127.34 - 133.99: 173 Bond angle restraints: 8408 Sorted by residual: angle pdb=" C TYR B 361 " pdb=" N LYS B 362 " pdb=" CA LYS B 362 " ideal model delta sigma weight residual 121.70 126.76 -5.06 1.80e+00 3.09e-01 7.89e+00 angle pdb=" C ASP B 166 " pdb=" N GLU B 167 " pdb=" CA GLU B 167 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.68e+00 angle pdb=" C SER B 113 " pdb=" N GLU B 114 " pdb=" CA GLU B 114 " ideal model delta sigma weight residual 122.07 124.77 -2.70 1.43e+00 4.89e-01 3.57e+00 angle pdb=" C HIS A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta sigma weight residual 122.08 124.50 -2.42 1.47e+00 4.63e-01 2.71e+00 angle pdb=" CA GLU B 167 " pdb=" CB GLU B 167 " pdb=" CG GLU B 167 " ideal model delta sigma weight residual 114.10 117.33 -3.23 2.00e+00 2.50e-01 2.60e+00 ... (remaining 8403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.18: 3323 19.18 - 38.35: 132 38.35 - 57.53: 63 57.53 - 76.70: 67 76.70 - 95.88: 2 Dihedral angle restraints: 3587 sinusoidal: 2015 harmonic: 1572 Sorted by residual: dihedral pdb=" CA LEU B 35 " pdb=" CB LEU B 35 " pdb=" CG LEU B 35 " pdb=" CD1 LEU B 35 " ideal model delta sinusoidal sigma weight residual 180.00 134.67 45.33 3 1.50e+01 4.44e-03 8.15e+00 dihedral pdb=" CA LEU A 104 " pdb=" CB LEU A 104 " pdb=" CG LEU A 104 " pdb=" CD1 LEU A 104 " ideal model delta sinusoidal sigma weight residual 180.00 140.47 39.53 3 1.50e+01 4.44e-03 7.01e+00 dihedral pdb=" O4' A C 7 " pdb=" C1' A C 7 " pdb=" N9 A C 7 " pdb=" C4 A C 7 " ideal model delta sinusoidal sigma weight residual -106.00 -142.86 36.86 1 1.70e+01 3.46e-03 6.64e+00 ... (remaining 3584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 687 0.025 - 0.049: 181 0.049 - 0.074: 52 0.074 - 0.098: 33 0.098 - 0.123: 36 Chirality restraints: 989 Sorted by residual: chirality pdb=" CA VAL B 98 " pdb=" N VAL B 98 " pdb=" C VAL B 98 " pdb=" CB VAL B 98 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL B 16 " pdb=" N VAL B 16 " pdb=" C VAL B 16 " pdb=" CB VAL B 16 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 986 not shown) Planarity restraints: 831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 59 " -0.013 2.00e-02 2.50e+03 6.11e-03 1.12e+00 pdb=" N9 G C 59 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 59 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 59 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G C 59 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 59 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 59 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 228 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.11e-01 pdb=" N PRO A 229 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 318 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.97e-01 pdb=" N PRO B 319 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " -0.012 5.00e-02 4.00e+02 ... (remaining 828 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1350 2.80 - 3.32: 5002 3.32 - 3.85: 10049 3.85 - 4.37: 11700 4.37 - 4.90: 18273 Nonbonded interactions: 46374 Sorted by model distance: nonbonded pdb=" ND1 HIS B 187 " pdb=" OG SER B 208 " model vdw 2.270 2.520 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 166 " model vdw 2.275 2.440 nonbonded pdb=" OP1 U C 60 " pdb=" N4 C C 61 " model vdw 2.296 2.520 nonbonded pdb=" O6 G C 10 " pdb=" N2 G C 45 " model vdw 2.303 2.520 nonbonded pdb=" OG1 THR B 188 " pdb=" OD2 ASP B 210 " model vdw 2.311 2.440 ... (remaining 46369 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=0.00 max=1.00 mean=0.99 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.920 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.001 0.020 5973 Z= 0.082 Angle : 0.366 5.055 8408 Z= 0.182 Chirality : 0.034 0.123 989 Planarity : 0.002 0.024 831 Dihedral : 15.506 95.877 2571 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.64 % Allowed : 5.77 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.53 (0.38), residues: 534 helix: 1.29 (0.58), residues: 103 sheet: 1.77 (0.39), residues: 185 loop : 0.37 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 206 HIS 0.002 0.000 HIS A 210 PHE 0.009 0.001 PHE A 166 TYR 0.004 0.001 TYR B 361 ARG 0.002 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9241 (t) cc_final: 0.8861 (p) REVERT: A 114 ASP cc_start: 0.9260 (t0) cc_final: 0.9017 (t0) REVERT: A 115 TYR cc_start: 0.9439 (t80) cc_final: 0.8910 (t80) REVERT: A 118 ASP cc_start: 0.9329 (m-30) cc_final: 0.9065 (m-30) REVERT: A 175 ILE cc_start: 0.9475 (mt) cc_final: 0.9115 (tp) REVERT: B 71 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8744 (tppt) REVERT: B 122 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8545 (ttpp) outliers start: 3 outliers final: 0 residues processed: 51 average time/residue: 0.1863 time to fit residues: 12.5593 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5973 Z= 0.366 Angle : 0.593 5.963 8408 Z= 0.299 Chirality : 0.039 0.138 989 Planarity : 0.003 0.023 831 Dihedral : 18.348 97.497 1564 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.92 % Allowed : 8.97 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.25 (0.39), residues: 534 helix: 1.22 (0.56), residues: 103 sheet: 1.64 (0.39), residues: 179 loop : 0.12 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 206 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.002 PHE B 271 TYR 0.008 0.001 TYR A 150 ARG 0.003 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 27 time to evaluate : 0.559 Fit side-chains REVERT: A 115 TYR cc_start: 0.9517 (t80) cc_final: 0.9272 (t80) REVERT: A 147 ASN cc_start: 0.9589 (m110) cc_final: 0.9368 (m-40) REVERT: A 175 ILE cc_start: 0.9589 (mt) cc_final: 0.9341 (tp) REVERT: B 71 LYS cc_start: 0.9441 (tmtt) cc_final: 0.9148 (tppt) REVERT: B 87 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8707 (tt) outliers start: 9 outliers final: 3 residues processed: 33 average time/residue: 0.1863 time to fit residues: 8.4836 Evaluate side-chains 21 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 192 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5973 Z= 0.402 Angle : 0.606 5.612 8408 Z= 0.310 Chirality : 0.040 0.173 989 Planarity : 0.004 0.033 831 Dihedral : 18.507 98.696 1564 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.35 % Allowed : 9.83 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.67 (0.37), residues: 534 helix: 1.18 (0.54), residues: 95 sheet: 1.37 (0.39), residues: 176 loop : -0.48 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 206 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.002 PHE B 271 TYR 0.009 0.001 TYR A 150 ARG 0.004 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 22 time to evaluate : 0.529 Fit side-chains REVERT: A 95 SER cc_start: 0.9360 (t) cc_final: 0.9085 (p) REVERT: A 115 TYR cc_start: 0.9528 (t80) cc_final: 0.8973 (t80) REVERT: A 175 ILE cc_start: 0.9590 (mt) cc_final: 0.9297 (tp) outliers start: 11 outliers final: 5 residues processed: 30 average time/residue: 0.1811 time to fit residues: 7.5972 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5973 Z= 0.263 Angle : 0.503 7.447 8408 Z= 0.256 Chirality : 0.038 0.187 989 Planarity : 0.003 0.033 831 Dihedral : 18.371 97.528 1564 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.92 % Allowed : 10.68 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 534 helix: 1.53 (0.55), residues: 98 sheet: 1.41 (0.39), residues: 176 loop : -0.45 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 206 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE A 166 TYR 0.005 0.001 TYR A 150 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.597 Fit side-chains REVERT: A 95 SER cc_start: 0.9275 (t) cc_final: 0.8989 (p) REVERT: A 115 TYR cc_start: 0.9495 (t80) cc_final: 0.9023 (t80) REVERT: A 140 ASN cc_start: 0.9257 (t0) cc_final: 0.8884 (t0) REVERT: A 175 ILE cc_start: 0.9592 (mt) cc_final: 0.9292 (tp) REVERT: B 168 LYS cc_start: 0.9277 (mtmm) cc_final: 0.9064 (mtmm) outliers start: 9 outliers final: 4 residues processed: 29 average time/residue: 0.1952 time to fit residues: 7.8743 Evaluate side-chains 21 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 17 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5973 Z= 0.180 Angle : 0.447 6.932 8408 Z= 0.228 Chirality : 0.037 0.184 989 Planarity : 0.003 0.029 831 Dihedral : 18.293 96.644 1564 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.14 % Allowed : 9.40 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.91 (0.38), residues: 534 helix: 1.79 (0.57), residues: 98 sheet: 1.28 (0.39), residues: 178 loop : -0.33 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 344 HIS 0.002 0.001 HIS B 225 PHE 0.012 0.001 PHE A 166 TYR 0.004 0.000 TYR A 150 ARG 0.001 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 19 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9205 (t) cc_final: 0.8914 (p) REVERT: A 115 TYR cc_start: 0.9486 (t80) cc_final: 0.9257 (t80) REVERT: A 140 ASN cc_start: 0.9206 (t0) cc_final: 0.8806 (t0) REVERT: A 175 ILE cc_start: 0.9557 (mt) cc_final: 0.9256 (tp) REVERT: A 264 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8975 (mm) outliers start: 10 outliers final: 4 residues processed: 27 average time/residue: 0.1852 time to fit residues: 7.0288 Evaluate side-chains 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5973 Z= 0.390 Angle : 0.588 6.136 8408 Z= 0.297 Chirality : 0.040 0.183 989 Planarity : 0.003 0.035 831 Dihedral : 18.494 98.539 1564 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.56 % Allowed : 10.47 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.55 (0.37), residues: 534 helix: 1.39 (0.55), residues: 95 sheet: 1.13 (0.38), residues: 176 loop : -0.54 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.002 PHE A 166 TYR 0.006 0.001 TYR B 269 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 21 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9398 (t) cc_final: 0.9099 (p) REVERT: A 115 TYR cc_start: 0.9520 (t80) cc_final: 0.9305 (t80) REVERT: A 140 ASN cc_start: 0.9329 (t0) cc_final: 0.8938 (t0) REVERT: A 175 ILE cc_start: 0.9577 (mt) cc_final: 0.9313 (tp) REVERT: A 264 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9100 (mm) outliers start: 12 outliers final: 6 residues processed: 30 average time/residue: 0.1880 time to fit residues: 7.9506 Evaluate side-chains 27 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5973 Z= 0.200 Angle : 0.468 5.983 8408 Z= 0.239 Chirality : 0.038 0.184 989 Planarity : 0.003 0.030 831 Dihedral : 18.433 97.389 1564 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.50 % Allowed : 10.68 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.37), residues: 534 helix: 1.60 (0.56), residues: 98 sheet: 1.09 (0.38), residues: 176 loop : -0.55 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.002 0.001 HIS B 187 PHE 0.012 0.001 PHE A 166 TYR 0.004 0.001 TYR B 269 ARG 0.001 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9261 (t) cc_final: 0.8987 (p) REVERT: A 115 TYR cc_start: 0.9490 (t80) cc_final: 0.9287 (t80) REVERT: A 140 ASN cc_start: 0.9240 (t0) cc_final: 0.8842 (t0) REVERT: A 175 ILE cc_start: 0.9505 (mt) cc_final: 0.9176 (tp) REVERT: A 264 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9044 (mm) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.2068 time to fit residues: 7.1243 Evaluate side-chains 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5973 Z= 0.187 Angle : 0.466 6.036 8408 Z= 0.236 Chirality : 0.037 0.185 989 Planarity : 0.003 0.028 831 Dihedral : 18.340 96.953 1564 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 10.26 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.65 (0.37), residues: 534 helix: 1.64 (0.57), residues: 98 sheet: 1.15 (0.38), residues: 174 loop : -0.53 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 293 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE A 166 TYR 0.004 0.001 TYR B 269 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9224 (t) cc_final: 0.8938 (p) REVERT: A 140 ASN cc_start: 0.9220 (t0) cc_final: 0.8813 (t0) REVERT: A 175 ILE cc_start: 0.9521 (mt) cc_final: 0.9195 (tp) REVERT: A 264 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9074 (mm) outliers start: 8 outliers final: 5 residues processed: 25 average time/residue: 0.2037 time to fit residues: 7.1482 Evaluate side-chains 23 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 0.0050 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5973 Z= 0.182 Angle : 0.468 8.220 8408 Z= 0.234 Chirality : 0.037 0.184 989 Planarity : 0.002 0.028 831 Dihedral : 18.276 96.799 1564 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 10.04 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.65 (0.37), residues: 534 helix: 1.65 (0.57), residues: 98 sheet: 1.14 (0.38), residues: 176 loop : -0.54 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 293 HIS 0.002 0.001 HIS B 187 PHE 0.011 0.001 PHE A 166 TYR 0.014 0.001 TYR A 115 ARG 0.001 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9217 (t) cc_final: 0.8929 (p) REVERT: A 140 ASN cc_start: 0.9205 (t0) cc_final: 0.8787 (t0) REVERT: A 175 ILE cc_start: 0.9538 (mt) cc_final: 0.9219 (tp) REVERT: A 264 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9084 (mm) REVERT: B 346 MET cc_start: 0.8799 (mmm) cc_final: 0.8156 (mmm) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.2088 time to fit residues: 6.7450 Evaluate side-chains 23 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5973 Z= 0.247 Angle : 0.500 8.376 8408 Z= 0.251 Chirality : 0.038 0.178 989 Planarity : 0.003 0.029 831 Dihedral : 18.351 97.276 1564 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 10.26 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.48 (0.37), residues: 534 helix: 1.50 (0.56), residues: 98 sheet: 1.04 (0.38), residues: 176 loop : -0.65 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 166 TYR 0.004 0.001 TYR B 269 ARG 0.002 0.000 ARG B 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9333 (t) cc_final: 0.8996 (p) REVERT: A 140 ASN cc_start: 0.9245 (t0) cc_final: 0.8864 (t0) REVERT: A 175 ILE cc_start: 0.9535 (mt) cc_final: 0.9218 (tp) REVERT: A 264 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9135 (mm) REVERT: B 346 MET cc_start: 0.9237 (mmm) cc_final: 0.8514 (mmm) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.2239 time to fit residues: 7.1374 Evaluate side-chains 23 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.032875 restraints weight = 33112.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.033912 restraints weight = 16126.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034611 restraints weight = 10474.846| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5973 Z= 0.190 Angle : 0.470 8.478 8408 Z= 0.235 Chirality : 0.037 0.177 989 Planarity : 0.002 0.027 831 Dihedral : 18.310 96.731 1564 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 10.26 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.53 (0.37), residues: 534 helix: 1.61 (0.56), residues: 98 sheet: 1.02 (0.38), residues: 176 loop : -0.61 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 293 HIS 0.002 0.001 HIS B 187 PHE 0.011 0.001 PHE A 166 TYR 0.014 0.001 TYR A 115 ARG 0.001 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1052.95 seconds wall clock time: 20 minutes 6.75 seconds (1206.75 seconds total)