Starting phenix.real_space_refine on Sun Mar 10 22:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/03_2024/8d9k_27264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/03_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_27264/03_2024/8d9k_27264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/03_2024/8d9k_27264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/03_2024/8d9k_27264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/03_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-dev-5265/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: 3.82, per 1000 atoms: 0.67 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: 2.50 Conformation dependent library (CDL) restraints added in 914.6 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: 2.25 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: 2.12 Time building geometry restraints manager: 2.70 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: 3340 19.18 - 38.35: 148 38.35 - 57.53: 72 57.53 - 76.70: 81 76.70 - 95.88: 2 Dihedral angle restraints: 3643 sinusoidal: 2071 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 3640 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: 0.190 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: 0.940 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.880 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- 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 : 16.349 95.877 2627 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 : 0.632 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: 0.1887 time to fit residues: 12.8965 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 0.8579 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5973 Z= 0.383 Angle : 0.617 6.461 8408 Z= 0.310 Chirality : 0.040 0.146 989 Planarity : 0.003 0.024 831 Dihedral : 19.287 97.043 1620 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.92 % Allowed : 8.76 % Favored : 89.32 % 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 (0.38), residues: 534 helix: 1.60 (0.57), residues: 97 sheet: 1.61 (0.39), residues: 179 loop : 0.01 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.002 PHE B 271 TYR 0.009 0.001 TYR A 150 ARG 0.004 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 : 0.588 Fit side-chains REVERT: A 115 TYR cc_start: 0.9520 (t80) cc_final: 0.9281 (t80) REVERT: A 147 ASN cc_start: 0.9597 (m110) cc_final: 0.9348 (m-40) REVERT: A 175 ILE cc_start: 0.9588 (mt) cc_final: 0.9347 (tp) REVERT: B 71 LYS cc_start: 0.9450 (tmtt) cc_final: 0.9156 (tppt) outliers start: 9 outliers final: 3 residues processed: 33 average time/residue: 0.2107 time to fit residues: 9.6930 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR 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: 6.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 53 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: 0.8619 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5973 Z= 0.383 Angle : 0.598 5.522 8408 Z= 0.306 Chirality : 0.040 0.195 989 Planarity : 0.004 0.034 831 Dihedral : 19.452 98.068 1620 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 10.26 % Favored : 87.61 % 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: 0.68 (0.37), residues: 534 helix: 1.18 (0.54), residues: 95 sheet: 1.38 (0.39), residues: 176 loop : -0.46 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 32 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 22 time to evaluate : 0.611 Fit side-chains REVERT: A 95 SER cc_start: 0.9355 (t) cc_final: 0.9097 (p) REVERT: A 115 TYR cc_start: 0.9514 (t80) cc_final: 0.8940 (t80) REVERT: A 175 ILE cc_start: 0.9590 (mt) cc_final: 0.9292 (tp) outliers start: 10 outliers final: 5 residues processed: 28 average time/residue: 0.1877 time to fit residues: 7.4219 Evaluate side-chains 24 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8590 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5973 Z= 0.199 Angle : 0.465 5.541 8408 Z= 0.239 Chirality : 0.038 0.207 989 Planarity : 0.003 0.032 831 Dihedral : 19.258 96.131 1620 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 10.90 % 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: 0.95 (0.38), residues: 534 helix: 1.66 (0.56), residues: 98 sheet: 1.48 (0.39), residues: 176 loop : -0.37 (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 0.005 0.001 TYR B 38 ARG 0.002 0.000 ARG B 214 *********************** 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 26 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 18 time to evaluate : 0.573 Fit side-chains REVERT: A 95 SER cc_start: 0.9227 (t) cc_final: 0.8946 (p) REVERT: A 115 TYR cc_start: 0.9484 (t80) cc_final: 0.8998 (t80) REVERT: A 140 ASN cc_start: 0.9217 (t0) cc_final: 0.8833 (t0) REVERT: A 175 ILE cc_start: 0.9575 (mt) cc_final: 0.9259 (tp) REVERT: B 168 LYS cc_start: 0.9273 (mtmm) cc_final: 0.9071 (mtmm) outliers start: 8 outliers final: 3 residues processed: 26 average time/residue: 0.1902 time to fit residues: 6.9654 Evaluate side-chains 19 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 23 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8618 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5973 Z= 0.310 Angle : 0.526 4.727 8408 Z= 0.270 Chirality : 0.039 0.203 989 Planarity : 0.003 0.034 831 Dihedral : 19.319 97.565 1620 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.35 % Allowed : 9.40 % Favored : 88.25 % 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: 0.78 (0.38), residues: 534 helix: 1.53 (0.55), residues: 98 sheet: 1.33 (0.39), residues: 176 loop : -0.45 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 206 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 166 TYR 0.004 0.001 TYR A 150 ARG 0.003 0.000 ARG B 99 *********************** 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 26 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 15 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9312 (t) cc_final: 0.9013 (p) REVERT: A 115 TYR cc_start: 0.9507 (t80) cc_final: 0.9049 (t80) REVERT: A 175 ILE cc_start: 0.9593 (mt) cc_final: 0.9304 (tp) REVERT: A 264 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9085 (mm) outliers start: 11 outliers final: 5 residues processed: 25 average time/residue: 0.1907 time to fit residues: 6.7113 Evaluate side-chains 21 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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: 0.8591 moved from start: 0.3722 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= 0.173 Angle : 0.449 6.883 8408 Z= 0.230 Chirality : 0.037 0.201 989 Planarity : 0.002 0.028 831 Dihedral : 19.234 96.308 1620 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 10.04 % 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: 0.90 (0.38), residues: 534 helix: 1.76 (0.57), residues: 98 sheet: 1.42 (0.39), residues: 175 loop : -0.43 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE A 166 TYR 0.003 0.000 TYR B 269 ARG 0.003 0.000 ARG B 21 *********************** 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 27 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9203 (t) cc_final: 0.8929 (p) REVERT: A 115 TYR cc_start: 0.9484 (t80) cc_final: 0.9270 (t80) REVERT: A 140 ASN cc_start: 0.9179 (t0) cc_final: 0.8762 (t0) REVERT: A 175 ILE cc_start: 0.9564 (mt) cc_final: 0.9259 (tp) REVERT: A 264 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8978 (mm) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.1974 time to fit residues: 7.4640 Evaluate side-chains 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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 162 THR 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: 9.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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: 0.8617 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5973 Z= 0.290 Angle : 0.510 5.520 8408 Z= 0.261 Chirality : 0.038 0.197 989 Planarity : 0.003 0.030 831 Dihedral : 19.291 97.214 1620 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 0.71 (0.37), residues: 534 helix: 1.56 (0.55), residues: 98 sheet: 1.31 (0.39), residues: 174 loop : -0.54 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 216 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 166 TYR 0.016 0.001 TYR B 38 ARG 0.004 0.000 ARG B 21 *********************** 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 28 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 17 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9344 (t) cc_final: 0.9017 (p) REVERT: A 115 TYR cc_start: 0.9502 (t80) cc_final: 0.9301 (t80) REVERT: A 140 ASN cc_start: 0.9256 (t0) cc_final: 0.8861 (t0) REVERT: A 175 ILE cc_start: 0.9545 (mt) cc_final: 0.9230 (tp) REVERT: A 264 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9084 (mm) outliers start: 11 outliers final: 8 residues processed: 27 average time/residue: 0.1889 time to fit residues: 7.2101 Evaluate side-chains 26 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 17 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 169 THR 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 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: 7.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5973 Z= 0.158 Angle : 0.441 5.917 8408 Z= 0.226 Chirality : 0.037 0.192 989 Planarity : 0.002 0.027 831 Dihedral : 19.148 95.791 1620 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.77 (0.38), residues: 534 helix: 1.75 (0.57), residues: 98 sheet: 1.31 (0.39), residues: 174 loop : -0.53 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 344 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE A 166 TYR 0.025 0.001 TYR B 38 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 28 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 20 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9174 (t) cc_final: 0.8902 (p) REVERT: A 140 ASN cc_start: 0.9168 (t0) cc_final: 0.8919 (t0) REVERT: A 147 ASN cc_start: 0.9474 (m110) cc_final: 0.9187 (m-40) REVERT: A 175 ILE cc_start: 0.9541 (mt) cc_final: 0.9219 (tp) REVERT: A 264 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8985 (mm) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.1979 time to fit residues: 7.7086 Evaluate side-chains 24 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8587 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5973 Z= 0.169 Angle : 0.456 5.594 8408 Z= 0.231 Chirality : 0.037 0.189 989 Planarity : 0.002 0.025 831 Dihedral : 19.119 95.894 1620 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 10.68 % 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: 0.71 (0.37), residues: 534 helix: 1.66 (0.57), residues: 98 sheet: 1.27 (0.38), residues: 174 loop : -0.54 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.001 PHE A 166 TYR 0.018 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 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9196 (t) cc_final: 0.8915 (p) REVERT: A 140 ASN cc_start: 0.9188 (t0) cc_final: 0.8759 (t0) REVERT: A 175 ILE cc_start: 0.9546 (mt) cc_final: 0.9228 (tp) REVERT: A 264 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9041 (mm) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.2075 time to fit residues: 7.2626 Evaluate side-chains 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.8571 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5973 Z= 0.144 Angle : 0.459 8.434 8408 Z= 0.228 Chirality : 0.037 0.182 989 Planarity : 0.002 0.023 831 Dihedral : 19.038 94.962 1620 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.50 % Allowed : 10.90 % Favored : 87.61 % 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: 0.77 (0.37), residues: 534 helix: 1.70 (0.57), residues: 98 sheet: 1.31 (0.38), residues: 174 loop : -0.50 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.001 0.000 HIS A 165 PHE 0.011 0.001 PHE A 166 TYR 0.009 0.001 TYR B 38 ARG 0.002 0.000 ARG B 21 ********************** 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 27 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9178 (t) cc_final: 0.8895 (p) REVERT: A 140 ASN cc_start: 0.9194 (t0) cc_final: 0.8964 (t0) REVERT: A 175 ILE cc_start: 0.9540 (mt) cc_final: 0.9218 (tp) REVERT: A 264 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9090 (mm) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.2207 time to fit residues: 7.8230 Evaluate side-chains 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.033792 restraints weight = 32755.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034853 restraints weight = 16029.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035563 restraints weight = 10338.131| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3934 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= 0.170 Angle : 0.460 8.229 8408 Z= 0.230 Chirality : 0.037 0.179 989 Planarity : 0.002 0.024 831 Dihedral : 19.048 95.345 1620 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.14 % Allowed : 10.26 % Favored : 87.61 % 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: 0.75 (0.37), residues: 534 helix: 1.71 (0.57), residues: 98 sheet: 1.23 (0.39), residues: 175 loop : -0.49 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 344 HIS 0.001 0.001 HIS B 187 PHE 0.011 0.001 PHE A 166 TYR 0.017 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: 1115.37 seconds wall clock time: 21 minutes 12.43 seconds (1272.43 seconds total)