Starting phenix.real_space_refine on Mon Nov 13 22:06:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/11_2023/8d9k_27264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/11_2023/8d9k_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_27264/11_2023/8d9k_27264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/11_2023/8d9k_27264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/11_2023/8d9k_27264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9k_27264/11_2023/8d9k_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-1.21rc1-5144/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: 4.22, per 1000 atoms: 0.74 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: 2.52 Conformation dependent library (CDL) restraints added in 929.6 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: 2.19 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: 2.06 Time building geometry restraints manager: 2.65 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: 3258 19.18 - 38.35: 111 38.35 - 57.53: 15 57.53 - 76.70: 1 76.70 - 95.88: 2 Dihedral angle restraints: 3387 sinusoidal: 1815 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 3384 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: 0.120 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: 22.320 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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 : 9.120 95.877 2371 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 *********************** 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 : 0.568 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 51 average time/residue: 0.1908 time to fit residues: 12.9445 Evaluate side-chains 18 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6987 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.8593 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5973 Z= 0.427 Angle : 0.669 7.014 8408 Z= 0.337 Chirality : 0.041 0.135 989 Planarity : 0.004 0.028 831 Dihedral : 10.072 97.810 1364 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.56 % Allowed : 8.97 % 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: 1.06 (0.38), residues: 534 helix: 1.42 (0.58), residues: 94 sheet: 1.58 (0.39), residues: 177 loop : -0.15 (0.40), residues: 263 *********************** 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 37 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.558 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 34 average time/residue: 0.1736 time to fit residues: 8.3902 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 15 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0525 time to fit residues: 1.1799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 53 optimal weight: 0.0040 overall best weight: 1.8396 ------------------------------------------------------------------------------- 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: 0.8546 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5973 Z= 0.145 Angle : 0.450 7.889 8408 Z= 0.229 Chirality : 0.037 0.157 989 Planarity : 0.002 0.022 831 Dihedral : 9.677 94.884 1364 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.85 % Allowed : 11.32 % 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: 1.25 (0.38), residues: 534 helix: 1.86 (0.57), residues: 97 sheet: 1.49 (0.39), residues: 179 loop : -0.01 (0.41), residues: 258 *********************** 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 30 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.561 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.1851 time to fit residues: 7.5243 Evaluate side-chains 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1892 time to fit residues: 1.1569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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: 0.8561 moved from start: 0.2982 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= 0.195 Angle : 0.457 6.133 8408 Z= 0.233 Chirality : 0.037 0.155 989 Planarity : 0.002 0.019 831 Dihedral : 9.574 95.615 1364 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.07 % Allowed : 10.47 % 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: 1.19 (0.38), residues: 534 helix: 1.87 (0.57), residues: 97 sheet: 1.46 (0.39), residues: 178 loop : -0.09 (0.41), residues: 259 *********************** 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 24 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.490 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.1907 time to fit residues: 6.4194 Evaluate side-chains 18 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0534 time to fit residues: 0.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8540 moved from start: 0.2988 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= 0.128 Angle : 0.428 7.498 8408 Z= 0.216 Chirality : 0.037 0.157 989 Planarity : 0.002 0.022 831 Dihedral : 9.443 94.743 1364 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.28 % Allowed : 9.83 % Favored : 88.89 % 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: 1.18 (0.38), residues: 534 helix: 1.50 (0.58), residues: 103 sheet: 1.47 (0.38), residues: 178 loop : 0.02 (0.42), residues: 253 *********************** 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 27 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.592 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 26 average time/residue: 0.2021 time to fit residues: 7.3185 Evaluate side-chains 19 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0668 time to fit residues: 0.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.0000 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.2790 ------------------------------------------------------------------------------- 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: 0.8551 moved from start: 0.3102 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= 0.162 Angle : 0.446 7.787 8408 Z= 0.223 Chirality : 0.037 0.159 989 Planarity : 0.002 0.021 831 Dihedral : 9.446 95.272 1364 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.43 % Allowed : 11.32 % 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: 1.13 (0.38), residues: 534 helix: 1.45 (0.57), residues: 103 sheet: 1.40 (0.38), residues: 178 loop : 0.03 (0.42), residues: 253 *********************** 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 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.556 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.2154 time to fit residues: 6.6070 Evaluate side-chains 20 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0535 time to fit residues: 0.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.3356 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= 0.207 Angle : 0.468 7.820 8408 Z= 0.236 Chirality : 0.037 0.161 989 Planarity : 0.002 0.020 831 Dihedral : 9.566 96.166 1364 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.43 % Allowed : 11.11 % 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: 1.00 (0.38), residues: 534 helix: 1.40 (0.57), residues: 103 sheet: 1.29 (0.39), residues: 178 loop : -0.05 (0.42), residues: 253 *********************** 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 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.559 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.2194 time to fit residues: 6.7837 Evaluate side-chains 19 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 7.2588 ------------------------------------------------------------------------------- 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: 0.8632 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5973 Z= 0.460 Angle : 0.668 6.407 8408 Z= 0.338 Chirality : 0.042 0.168 989 Planarity : 0.004 0.034 831 Dihedral : 10.365 99.094 1364 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.28 % Allowed : 10.47 % 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: 0.34 (0.36), residues: 534 helix: 1.09 (0.54), residues: 95 sheet: 0.96 (0.38), residues: 179 loop : -0.60 (0.38), residues: 260 *********************** 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 29 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.700 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 28 average time/residue: 0.1930 time to fit residues: 7.6149 Evaluate side-chains 24 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0563 time to fit residues: 1.0399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8573 moved from start: 0.3937 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= 0.143 Angle : 0.474 7.557 8408 Z= 0.239 Chirality : 0.038 0.167 989 Planarity : 0.003 0.027 831 Dihedral : 9.962 96.421 1364 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.21 % Allowed : 11.75 % 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: 1.64 (0.56), residues: 98 sheet: 1.06 (0.39), residues: 178 loop : -0.39 (0.39), residues: 258 *********************** 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 22 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.551 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.2331 time to fit residues: 6.7814 Evaluate side-chains 19 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8594 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5973 Z= 0.242 Angle : 0.500 6.945 8408 Z= 0.255 Chirality : 0.038 0.169 989 Planarity : 0.003 0.030 831 Dihedral : 9.965 97.119 1364 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.21 % Allowed : 11.75 % 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: 0.57 (0.37), residues: 534 helix: 1.54 (0.56), residues: 98 sheet: 0.98 (0.39), residues: 178 loop : -0.49 (0.39), residues: 258 ********************** 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 25 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.550 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.2030 time to fit residues: 7.0453 Evaluate side-chains 23 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.046795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.034338 restraints weight = 32317.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.035427 restraints weight = 15971.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036144 restraints weight = 10343.831| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5973 Z= 0.113 Angle : 0.449 7.477 8408 Z= 0.226 Chirality : 0.037 0.167 989 Planarity : 0.002 0.025 831 Dihedral : 9.719 95.095 1364 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 11.97 % 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: 0.79 (0.37), residues: 534 helix: 1.68 (0.57), residues: 98 sheet: 1.11 (0.39), residues: 173 loop : -0.29 (0.39), residues: 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.70 seconds wall clock time: 21 minutes 2.61 seconds (1262.61 seconds total)