Starting phenix.real_space_refine (version: dev) on Thu May 12 20:28:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/05_2022/6x0l_21978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/05_2022/6x0l_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_21978/05_2022/6x0l_21978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/05_2022/6x0l_21978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/05_2022/6x0l_21978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0l_21978/05_2022/6x0l_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 20, 'TRANS': 452, 'PCIS': 1} 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: 5.12, per 1000 atoms: 0.64 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: 3.61 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: 2.28 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: 2.62 Time building geometry restraints manager: 3.87 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: 0.010 Normalize map: mean=0, sd=1: 4.000 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: 23.350 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 28.410 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.050 ------------------------------------------------------------------------------- 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 : 21.49 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 : 0.954 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2249 time to fit residues: 53.0511 Evaluate side-chains 108 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2112 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 371 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8291 Z= 0.245 Angle : 0.725 13.128 11352 Z= 0.386 Chirality : 0.043 0.146 1220 Planarity : 0.005 0.067 1329 Dihedral : 19.622 162.392 1350 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.81 % 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: -0.36 (0.27), residues: 884 helix: 0.62 (0.28), residues: 320 sheet: -0.29 (0.38), residues: 161 loop : -0.85 (0.31), residues: 403 *********************** 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 135 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.978 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 0.1947 time to fit residues: 34.9320 Evaluate side-chains 114 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0866 time to fit residues: 3.1065 ------------------------------------------------------------------------------- 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: 2.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- 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 147 HIS ** P 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 8291 Z= 0.320 Angle : 0.764 13.566 11352 Z= 0.403 Chirality : 0.044 0.167 1220 Planarity : 0.005 0.064 1329 Dihedral : 19.543 160.274 1350 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 2.42 % 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: -0.44 (0.27), residues: 884 helix: 0.67 (0.28), residues: 319 sheet: -0.34 (0.40), residues: 162 loop : -1.00 (0.30), residues: 403 *********************** 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 125 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.980 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.1929 time to fit residues: 32.2895 Evaluate side-chains 107 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0985 time to fit residues: 3.0407 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 261 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 8291 Z= 0.409 Angle : 0.830 17.168 11352 Z= 0.443 Chirality : 0.048 0.157 1220 Planarity : 0.005 0.048 1329 Dihedral : 19.683 155.725 1350 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 3.57 % 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: -0.71 (0.28), residues: 884 helix: 0.34 (0.28), residues: 320 sheet: -0.38 (0.41), residues: 161 loop : -1.11 (0.31), residues: 403 *********************** 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 127 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 116 average time/residue: 0.1826 time to fit residues: 30.0262 Evaluate side-chains 107 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0815 time to fit residues: 3.1290 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 343 HIS ** 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: 0.6850 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 8291 Z= 0.242 Angle : 0.727 17.334 11352 Z= 0.385 Chirality : 0.043 0.154 1220 Planarity : 0.004 0.084 1329 Dihedral : 19.517 156.554 1350 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 3.19 % 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: -0.38 (0.28), residues: 884 helix: 0.65 (0.29), residues: 321 sheet: -0.22 (0.42), residues: 155 loop : -0.93 (0.31), residues: 408 *********************** 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 129 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 116 average time/residue: 0.1960 time to fit residues: 31.6566 Evaluate side-chains 100 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1114 time to fit residues: 2.9605 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 343 HIS ** 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 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: 0.6915 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.132 8291 Z= 0.328 Angle : 0.791 17.066 11352 Z= 0.421 Chirality : 0.045 0.163 1220 Planarity : 0.005 0.055 1329 Dihedral : 19.519 157.299 1350 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 2.93 % 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: -0.63 (0.28), residues: 884 helix: 0.40 (0.28), residues: 321 sheet: -0.43 (0.42), residues: 155 loop : -1.01 (0.31), residues: 408 *********************** 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 119 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.969 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 112 average time/residue: 0.1886 time to fit residues: 29.7449 Evaluate side-chains 99 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0827 time to fit residues: 2.8813 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 343 HIS ** 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 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: 0.6895 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.278 8291 Z= 0.370 Angle : 0.815 24.311 11352 Z= 0.440 Chirality : 0.044 0.227 1220 Planarity : 0.005 0.094 1329 Dihedral : 19.534 157.948 1350 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.53 % 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: -0.60 (0.28), residues: 884 helix: 0.49 (0.28), residues: 321 sheet: -0.52 (0.41), residues: 154 loop : -1.00 (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 107 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 0.2238 time to fit residues: 31.4259 Evaluate side-chains 98 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0746 time to fit residues: 2.1711 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 110 ASN ** 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: 0.6915 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 8291 Z= 0.309 Angle : 0.788 15.594 11352 Z= 0.414 Chirality : 0.044 0.195 1220 Planarity : 0.005 0.073 1329 Dihedral : 19.567 158.999 1350 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % 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: -0.70 (0.28), residues: 884 helix: 0.44 (0.28), residues: 321 sheet: -0.76 (0.42), residues: 145 loop : -1.01 (0.31), residues: 418 *********************** 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 102 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.959 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 98 average time/residue: 0.2012 time to fit residues: 27.7028 Evaluate side-chains 90 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0889 time to fit residues: 1.7825 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.389 8291 Z= 0.449 Angle : 1.027 57.655 11352 Z= 0.512 Chirality : 0.042 0.181 1220 Planarity : 0.006 0.140 1329 Dihedral : 19.313 160.379 1350 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.17 (0.28), residues: 884 helix: 0.97 (0.29), residues: 314 sheet: -0.43 (0.41), residues: 155 loop : -0.77 (0.31), residues: 415 *********************** 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 103 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.946 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.1977 time to fit residues: 27.7400 Evaluate side-chains 90 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 1.4551 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.511 8291 Z= 0.538 Angle : 0.967 46.629 11352 Z= 0.490 Chirality : 0.042 0.180 1220 Planarity : 0.005 0.112 1329 Dihedral : 19.274 160.882 1350 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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: -0.22 (0.28), residues: 884 helix: 0.93 (0.29), residues: 316 sheet: -0.48 (0.41), residues: 155 loop : -0.79 (0.32), residues: 413 ********************** 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 90 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.934 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1991 time to fit residues: 25.0069 Evaluate side-chains 88 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0940 time to fit residues: 1.4275 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 343 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.104564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.096555 restraints weight = 32795.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.097987 restraints weight = 18714.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.099015 restraints weight = 12294.965| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.540 8291 Z= 0.550 Angle : 0.945 40.112 11352 Z= 0.480 Chirality : 0.043 0.179 1220 Planarity : 0.005 0.101 1329 Dihedral : 19.280 164.667 1350 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.12 (0.29), residues: 884 helix: 1.00 (0.29), residues: 316 sheet: -0.42 (0.41), residues: 155 loop : -0.74 (0.32), residues: 413 =============================================================================== Job complete usr+sys time: 1737.49 seconds wall clock time: 32 minutes 32.45 seconds (1952.45 seconds total)