Starting phenix.real_space_refine (version: dev) on Sat Feb 18 11:07:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/02_2023/6x0l_21978.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 194": "OE1" <-> "OE2" Residue "O GLU 198": "OE1" <-> "OE2" Residue "O GLU 273": "OE1" <-> "OE2" Residue "O GLU 327": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "P ARG 137": "NH1" <-> "NH2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 277": "NH1" <-> "NH2" Residue "P GLU 322": "OE1" <-> "OE2" Residue "P ARG 350": "NH1" <-> "NH2" Residue "P GLU 362": "OE1" <-> "OE2" Residue "R GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8037 Number of models: 1 Model: "" Number of chains: 7 Chain: "O" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "P" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3798 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 929 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Chain: "J" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "i" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "j" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 4.89, per 1000 atoms: 0.61 Number of scatterers: 8037 At special positions: 0 Unit cell: (115.54, 109.18, 91.16, 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 45 16.00 P 40 15.00 O 1584 8.00 N 1379 7.00 C 4989 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: 3.65 Conformation dependent library (CDL) restraints added in 1.0 seconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.4% alpha, 19.8% beta 20 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'O' and resid 37 through 46 removed outlier: 3.895A pdb=" N VAL O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 64 removed outlier: 3.974A pdb=" N TYR O 54 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 77 Processing helix chain 'O' and resid 82 through 88 removed outlier: 3.500A pdb=" N ILE O 86 " --> pdb=" O GLY O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 176 removed outlier: 3.785A pdb=" N LYS O 174 " --> pdb=" O THR O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 200 Processing helix chain 'O' and resid 207 through 217 Processing helix chain 'O' and resid 244 through 257 Processing helix chain 'O' and resid 260 through 268 Processing helix chain 'O' and resid 268 through 284 Processing helix chain 'O' and resid 286 through 301 removed outlier: 4.404A pdb=" N GLY O 290 " --> pdb=" O ASP O 286 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY O 294 " --> pdb=" O GLY O 290 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 304 No H-bonds generated for 'chain 'O' and resid 302 through 304' Processing helix chain 'O' and resid 305 through 320 Proline residue: O 314 - end of helix Processing helix chain 'O' and resid 322 through 335 Processing helix chain 'P' and resid 155 through 172 Processing helix chain 'P' and resid 222 through 233 Processing helix chain 'P' and resid 234 through 248 removed outlier: 3.532A pdb=" N LYS P 246 " --> pdb=" O MET P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 278 removed outlier: 3.868A pdb=" N ALA P 278 " --> pdb=" O ASP P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 296 removed outlier: 3.559A pdb=" N MET P 286 " --> pdb=" O GLY P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 334 removed outlier: 3.583A pdb=" N LEU P 314 " --> pdb=" O THR P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 353 removed outlier: 4.088A pdb=" N GLN P 347 " --> pdb=" O HIS P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 376 Processing helix chain 'P' and resid 398 through 403 removed outlier: 3.764A pdb=" N ALA P 402 " --> pdb=" O GLY P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 421 through 429 removed outlier: 3.745A pdb=" N ILE P 425 " --> pdb=" O ASN P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 442 removed outlier: 3.575A pdb=" N GLY P 441 " --> pdb=" O PRO P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 459 removed outlier: 3.588A pdb=" N SER P 457 " --> pdb=" O MET P 453 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 462 No H-bonds generated for 'chain 'P' and resid 460 through 462' Processing helix chain 'P' and resid 511 through 515 Processing helix chain 'P' and resid 550 through 552 No H-bonds generated for 'chain 'P' and resid 550 through 552' Processing helix chain 'R' and resid 155 through 172 Processing sheet with id=AA1, first strand: chain 'O' and resid 79 through 80 removed outlier: 6.690A pdb=" N MET O 129 " --> pdb=" O ILE O 118 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE O 120 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR O 127 " --> pdb=" O ILE O 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR O 142 " --> pdb=" O PHE O 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 92 through 94 removed outlier: 3.711A pdb=" N GLY P 139 " --> pdb=" O TYR P 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 92 through 94 removed outlier: 4.695A pdb=" N MET P 105 " --> pdb=" O LEU P 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'P' and resid 354 through 358 removed outlier: 5.159A pdb=" N MET P 386 " --> pdb=" O ASN P 565 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN P 565 " --> pdb=" O MET P 386 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU P 388 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN P 563 " --> pdb=" O LEU P 388 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG P 557 " --> pdb=" O VAL P 394 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS P 396 " --> pdb=" O ARG P 555 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ARG P 555 " --> pdb=" O LYS P 396 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU P 474 " --> pdb=" O ARG P 557 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU P 559 " --> pdb=" O LEU P 472 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU P 472 " --> pdb=" O LEU P 559 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS P 561 " --> pdb=" O GLY P 470 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY P 470 " --> pdb=" O LYS P 561 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU P 471 " --> pdb=" O SER P 417 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER P 417 " --> pdb=" O LEU P 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 448 through 450 removed outlier: 5.852A pdb=" N ASN P 483 " --> pdb=" O LYS P 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 529 through 530 removed outlier: 6.758A pdb=" N TYR P 543 " --> pdb=" O LYS P 507 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA P 509 " --> pdb=" O TYR P 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 516 through 518 Processing sheet with id=AA9, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 132 " --> pdb=" O CYS R 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.833A pdb=" N HIS R 93 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 96 through 97 332 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2121 1.33 - 1.45: 1667 1.45 - 1.57: 4354 1.57 - 1.69: 76 1.69 - 1.81: 73 Bond restraints: 8291 Sorted by residual: bond pdb=" CA PRO P 434 " pdb=" C PRO P 434 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" C1' DA i 82 " pdb=" N9 DA i 82 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA j -81 " pdb=" N9 DA j -81 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1' DA j -78 " pdb=" N9 DA j -78 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C PRO P 434 " pdb=" O PRO P 434 " ideal model delta sigma weight residual 1.246 1.219 0.026 8.50e-03 1.38e+04 9.71e+00 ... (remaining 8286 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.57: 339 105.57 - 112.67: 4250 112.67 - 119.78: 2872 119.78 - 126.89: 3698 126.89 - 134.00: 193 Bond angle restraints: 11352 Sorted by residual: angle pdb=" N THR O 93 " pdb=" CA THR O 93 " pdb=" C THR O 93 " ideal model delta sigma weight residual 113.18 108.03 5.15 1.33e+00 5.65e-01 1.50e+01 angle pdb=" N LYS O 174 " pdb=" CA LYS O 174 " pdb=" C LYS O 174 " ideal model delta sigma weight residual 112.90 108.19 4.71 1.31e+00 5.83e-01 1.29e+01 angle pdb=" CA LYS O 181 " pdb=" C LYS O 181 " pdb=" O LYS O 181 " ideal model delta sigma weight residual 122.63 118.17 4.46 1.29e+00 6.01e-01 1.19e+01 angle pdb=" C MET P 556 " pdb=" N ARG P 557 " pdb=" CA ARG P 557 " ideal model delta sigma weight residual 122.15 112.75 9.40 2.83e+00 1.25e-01 1.10e+01 angle pdb=" CA PRO P 434 " pdb=" C PRO P 434 " pdb=" O PRO P 434 " ideal model delta sigma weight residual 120.90 118.60 2.30 7.20e-01 1.93e+00 1.02e+01 ... (remaining 11347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 4596 34.73 - 69.46: 250 69.46 - 104.19: 10 104.19 - 138.92: 0 138.92 - 173.64: 1 Dihedral angle restraints: 4857 sinusoidal: 2250 harmonic: 2607 Sorted by residual: dihedral pdb=" CA GLY R 90 " pdb=" C GLY R 90 " pdb=" N LYS R 91 " pdb=" CA LYS R 91 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASN P 99 " pdb=" C ASN P 99 " pdb=" N ASP P 100 " pdb=" CA ASP P 100 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C4' DA J 80 " pdb=" C3' DA J 80 " pdb=" O3' DA J 80 " pdb=" P DT J 81 " ideal model delta sinusoidal sigma weight residual 220.00 46.36 173.64 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 4854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 827 0.044 - 0.089: 280 0.089 - 0.133: 94 0.133 - 0.177: 15 0.177 - 0.222: 4 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE O 182 " pdb=" N ILE O 182 " pdb=" C ILE O 182 " pdb=" CB ILE O 182 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE O 176 " pdb=" N ILE O 176 " pdb=" C ILE O 176 " pdb=" CB ILE O 176 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1' DA i 82 " pdb=" O4' DA i 82 " pdb=" C2' DA i 82 " pdb=" N9 DA i 82 " both_signs ideal model delta sigma weight residual False 2.42 2.23 0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1217 not shown) Planarity restraints: 1329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 425 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C ILE P 425 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE P 425 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU P 426 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 80 " -0.032 2.00e-02 2.50e+03 1.39e-02 5.29e+00 pdb=" N9 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" C8 DA i 80 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA i 80 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DA i 80 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA i 80 " -0.024 2.00e-02 2.50e+03 pdb=" N1 DA i 80 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA i 80 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA i 80 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA i 80 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT j -82 " 0.024 2.00e-02 2.50e+03 1.22e-02 3.73e+00 pdb=" N1 DT j -82 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT j -82 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT j -82 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DT j -82 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT j -82 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT j -82 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT j -82 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT j -82 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT j -82 " -0.015 2.00e-02 2.50e+03 ... (remaining 1326 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 125 2.63 - 3.20: 7616 3.20 - 3.77: 13417 3.77 - 4.33: 17912 4.33 - 4.90: 27606 Nonbonded interactions: 66676 Sorted by model distance: nonbonded pdb=" C2' DA i 77 " pdb=" C7 DT i 78 " model vdw 2.067 3.860 nonbonded pdb=" OE2 GLU O 114 " pdb=" OH TYR O 317 " model vdw 2.101 2.440 nonbonded pdb=" OH TYR P 119 " pdb=" OP1 DT j -82 " model vdw 2.119 2.440 nonbonded pdb=" OH TYR O 109 " pdb=" O GLY O 301 " model vdw 2.161 2.440 nonbonded pdb=" N GLY P 506 " pdb=" OD1 ASN P 544 " model vdw 2.174 2.520 ... (remaining 66671 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 45 5.16 5 C 4989 2.51 5 N 1379 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 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: 0.010 Extract box with map and model: 23.310 Check model and map are aligned: 0.110 Process input model: 26.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 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 : 0.005 0.074 8291 Z= 0.303 Angle : 0.850 9.403 11352 Z= 0.487 Chirality : 0.050 0.222 1220 Planarity : 0.005 0.035 1329 Dihedral : 18.723 173.644 3179 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.57 (0.26), residues: 884 helix: -0.58 (0.26), residues: 317 sheet: -0.40 (0.40), residues: 157 loop : -1.62 (0.29), residues: 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2448 time to fit residues: 57.5198 Evaluate side-chains 109 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 303 HIS ** O 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 GLN ** P 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 519 ASN P 553 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8291 Z= 0.209 Angle : 0.686 8.127 11352 Z= 0.365 Chirality : 0.042 0.136 1220 Planarity : 0.004 0.030 1329 Dihedral : 19.606 163.415 1350 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.27 (0.27), residues: 884 helix: 0.71 (0.28), residues: 321 sheet: -0.23 (0.38), residues: 161 loop : -0.81 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.935 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 134 average time/residue: 0.2030 time to fit residues: 37.2677 Evaluate side-chains 113 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0861 time to fit residues: 2.8892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 123 ASN ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 311 GLN ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 HIS ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 261 GLN P 371 GLN ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 459 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 8291 Z= 0.406 Angle : 0.811 8.252 11352 Z= 0.434 Chirality : 0.047 0.167 1220 Planarity : 0.005 0.054 1329 Dihedral : 19.633 159.614 1350 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 26.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 884 helix: 0.55 (0.27), residues: 319 sheet: -0.38 (0.39), residues: 168 loop : -1.07 (0.31), residues: 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 0.1888 time to fit residues: 31.7531 Evaluate side-chains 106 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0996 time to fit residues: 3.0669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.0470 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8291 Z= 0.218 Angle : 0.671 10.718 11352 Z= 0.356 Chirality : 0.043 0.164 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.462 157.233 1350 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.11 (0.28), residues: 884 helix: 0.90 (0.29), residues: 321 sheet: -0.12 (0.42), residues: 157 loop : -0.79 (0.31), residues: 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.966 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 0.2025 time to fit residues: 32.0070 Evaluate side-chains 103 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0847 time to fit residues: 2.5842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8291 Z= 0.190 Angle : 0.673 12.628 11352 Z= 0.347 Chirality : 0.041 0.166 1220 Planarity : 0.003 0.031 1329 Dihedral : 19.341 157.933 1350 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.01 (0.29), residues: 884 helix: 1.01 (0.29), residues: 321 sheet: -0.02 (0.43), residues: 156 loop : -0.74 (0.31), residues: 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.850 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.2058 time to fit residues: 30.4357 Evaluate side-chains 99 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1047 time to fit residues: 1.9890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 332 HIS ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 8291 Z= 0.345 Angle : 0.758 11.191 11352 Z= 0.399 Chirality : 0.045 0.194 1220 Planarity : 0.004 0.046 1329 Dihedral : 19.477 156.472 1350 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.39 (0.28), residues: 884 helix: 0.57 (0.28), residues: 320 sheet: -0.29 (0.43), residues: 154 loop : -0.84 (0.32), residues: 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.860 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 109 average time/residue: 0.1992 time to fit residues: 30.1601 Evaluate side-chains 102 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0852 time to fit residues: 2.7276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8291 Z= 0.233 Angle : 0.715 13.026 11352 Z= 0.368 Chirality : 0.043 0.203 1220 Planarity : 0.004 0.033 1329 Dihedral : 19.355 157.218 1350 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.20 (0.29), residues: 884 helix: 0.76 (0.29), residues: 320 sheet: -0.32 (0.43), residues: 155 loop : -0.69 (0.32), residues: 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.995 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 106 average time/residue: 0.2201 time to fit residues: 32.4669 Evaluate side-chains 95 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1050 time to fit residues: 2.4556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8291 Z= 0.270 Angle : 0.736 11.667 11352 Z= 0.381 Chirality : 0.044 0.204 1220 Planarity : 0.004 0.038 1329 Dihedral : 19.376 158.259 1350 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.29), residues: 884 helix: 0.64 (0.29), residues: 320 sheet: -0.50 (0.42), residues: 155 loop : -0.73 (0.32), residues: 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.947 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 102 average time/residue: 0.2437 time to fit residues: 33.4550 Evaluate side-chains 99 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1569 time to fit residues: 2.4126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 8291 Z= 0.226 Angle : 0.720 11.940 11352 Z= 0.370 Chirality : 0.043 0.210 1220 Planarity : 0.004 0.035 1329 Dihedral : 19.308 159.094 1350 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.23 (0.29), residues: 884 helix: 0.72 (0.29), residues: 321 sheet: -0.38 (0.43), residues: 155 loop : -0.68 (0.33), residues: 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.959 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.2319 time to fit residues: 31.1678 Evaluate side-chains 95 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1043 time to fit residues: 1.3930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 377 HIS ** P 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8291 Z= 0.199 Angle : 0.706 12.568 11352 Z= 0.362 Chirality : 0.042 0.207 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.193 160.177 1350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 884 helix: 0.91 (0.29), residues: 321 sheet: -0.45 (0.42), residues: 156 loop : -0.61 (0.33), residues: 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.942 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 103 average time/residue: 0.2212 time to fit residues: 31.0866 Evaluate side-chains 94 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0803 time to fit residues: 1.4393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 428 HIS ** R 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.105431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.097552 restraints weight = 31992.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.099028 restraints weight = 18915.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.100015 restraints weight = 12428.027| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8291 Z= 0.186 Angle : 0.725 12.717 11352 Z= 0.367 Chirality : 0.042 0.222 1220 Planarity : 0.003 0.030 1329 Dihedral : 19.118 163.088 1350 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.29), residues: 884 helix: 1.01 (0.29), residues: 321 sheet: -0.34 (0.42), residues: 156 loop : -0.54 (0.33), residues: 407 =============================================================================== Job complete usr+sys time: 1841.80 seconds wall clock time: 34 minutes 47.13 seconds (2087.13 seconds total)