Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 04:49:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvp_26815/10_2023/7uvp_26815_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3589 2.51 5 N 951 2.21 5 O 1094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 629": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5671 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5671 Unusual residues: {' MG': 1, 'GTP': 1} Inner-chain residues flagged as termini: ['pdbres="GLU A 718 "'] Classifications: {'peptide': 718, 'undetermined': 2, 'water': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 685, None: 3} Not linked: pdbres="GLU A 718 " pdbres="GTP A 901 " Not linked: pdbres="GTP A 901 " pdbres=" MG A 902 " Not linked: pdbres=" MG A 902 " pdbres="HOH A1001 " Time building chain proxies: 3.49, per 1000 atoms: 0.62 Number of scatterers: 5671 At special positions: 0 Unit cell: (73.692, 73.692, 128.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 3 15.00 Mg 1 11.99 O 1094 8.00 N 951 7.00 C 3589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 847.5 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 10 sheets defined 27.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.531A pdb=" N VAL A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.649A pdb=" N TYR A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 153 removed outlier: 4.217A pdb=" N GLU A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.981A pdb=" N ASP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 237 through 248 removed outlier: 4.205A pdb=" N GLY A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 242 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 559 through 572 removed outlier: 3.830A pdb=" N GLN A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 removed outlier: 3.523A pdb=" N ALA A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.859A pdb=" N GLU A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 158 through 160 removed outlier: 6.059A pdb=" N PHE A 252 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 129 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N PHE A 255 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 131 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 100 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 11 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 102 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 13 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 104 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 15 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ASN A 106 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS A 75 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 12 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN A 77 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 14 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 79 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY A 16 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 65 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 162 through 164 removed outlier: 4.027A pdb=" N LYS A 181 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 380 through 382 removed outlier: 4.494A pdb=" N SER A 324 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR A 304 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 322 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= E, first strand: chain 'A' and resid 348 through 350 Processing sheet with id= F, first strand: chain 'A' and resid 465 through 468 removed outlier: 4.610A pdb=" N THR A 440 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 439 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 434 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.575A pdb=" N ARG A 475 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 482 through 488 removed outlier: 3.682A pdb=" N ALA A 484 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 503 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 486 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 500 " --> pdb=" O LYS A 591 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 589 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 504 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL A 587 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 506 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 585 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 517 through 519 removed outlier: 3.982A pdb=" N TYR A 518 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 525 " --> pdb=" O TYR A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 691 through 693 removed outlier: 3.663A pdb=" N GLU A 657 " --> pdb=" O PHE A 660 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 664 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 653 " --> pdb=" O VAL A 664 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1864 1.34 - 1.46: 1135 1.46 - 1.58: 2714 1.58 - 1.69: 5 1.69 - 1.81: 61 Bond restraints: 5779 Sorted by residual: bond pdb=" CB PHE A 255 " pdb=" CG PHE A 255 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.08e-01 bond pdb=" C LYS A 471 " pdb=" N ILE A 472 " ideal model delta sigma weight residual 1.329 1.323 0.006 7.30e-03 1.88e+04 5.97e-01 bond pdb=" CA LYS A 405 " pdb=" C LYS A 405 " ideal model delta sigma weight residual 1.517 1.525 -0.008 1.07e-02 8.73e+03 5.04e-01 bond pdb=" C2' GTP A 901 " pdb=" C3' GTP A 901 " ideal model delta sigma weight residual 1.524 1.511 0.013 2.00e-02 2.50e+03 4.15e-01 bond pdb=" CE1 PHE A 255 " pdb=" CZ PHE A 255 " ideal model delta sigma weight residual 1.382 1.363 0.019 3.00e-02 1.11e+03 3.90e-01 ... (remaining 5774 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 166 106.51 - 113.39: 3108 113.39 - 120.27: 2018 120.27 - 127.16: 2457 127.16 - 134.04: 46 Bond angle restraints: 7795 Sorted by residual: angle pdb=" C GLU A 534 " pdb=" N ILE A 535 " pdb=" CA ILE A 535 " ideal model delta sigma weight residual 122.59 120.56 2.03 7.20e-01 1.93e+00 7.98e+00 angle pdb=" C1' GTP A 901 " pdb=" C2' GTP A 901 " pdb=" C3' GTP A 901 " ideal model delta sigma weight residual 111.00 104.51 6.49 3.00e+00 1.11e-01 4.68e+00 angle pdb=" N VAL A 275 " pdb=" CA VAL A 275 " pdb=" C VAL A 275 " ideal model delta sigma weight residual 106.42 109.51 -3.09 1.51e+00 4.39e-01 4.19e+00 angle pdb=" CA MET A 282 " pdb=" CB MET A 282 " pdb=" CG MET A 282 " ideal model delta sigma weight residual 114.10 117.75 -3.65 2.00e+00 2.50e-01 3.33e+00 angle pdb=" CA LYS A 124 " pdb=" CB LYS A 124 " pdb=" CG LYS A 124 " ideal model delta sigma weight residual 114.10 117.42 -3.32 2.00e+00 2.50e-01 2.75e+00 ... (remaining 7790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 3424 35.29 - 70.58: 80 70.58 - 105.86: 8 105.86 - 141.15: 2 141.15 - 176.44: 1 Dihedral angle restraints: 3515 sinusoidal: 1461 harmonic: 2054 Sorted by residual: dihedral pdb=" C8 GTP A 901 " pdb=" C1' GTP A 901 " pdb=" N9 GTP A 901 " pdb=" O4' GTP A 901 " ideal model delta sinusoidal sigma weight residual 104.59 -78.97 -176.44 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 901 " pdb=" O3A GTP A 901 " pdb=" PB GTP A 901 " pdb=" PA GTP A 901 " ideal model delta sinusoidal sigma weight residual 291.08 179.75 111.33 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" C4' GTP A 901 " pdb=" C5' GTP A 901 " pdb=" O5' GTP A 901 " pdb=" PA GTP A 901 " ideal model delta sinusoidal sigma weight residual 260.87 150.29 110.58 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 3512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 514 0.031 - 0.062: 213 0.062 - 0.093: 67 0.093 - 0.124: 47 0.124 - 0.156: 5 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL A 667 " pdb=" N VAL A 667 " pdb=" C VAL A 667 " pdb=" CB VAL A 667 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 843 not shown) Planarity restraints: 1012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 276 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 277 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 282 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO A 283 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 271 " 0.010 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 271 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 271 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 271 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 271 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 271 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 271 " 0.000 2.00e-02 2.50e+03 ... (remaining 1009 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.13: 4322 3.13 - 3.72: 8576 3.72 - 4.31: 11874 4.31 - 4.90: 19847 Nonbonded interactions: 44658 Sorted by model distance: nonbonded pdb=" O1B GTP A 901 " pdb="MG MG A 902 " model vdw 1.942 2.170 nonbonded pdb=" O3G GTP A 901 " pdb="MG MG A 902 " model vdw 1.987 2.170 nonbonded pdb=" O3B GTP A 901 " pdb="MG MG A 902 " model vdw 2.049 2.170 nonbonded pdb=" O LEU A 604 " pdb=" ND2 ASN A 608 " model vdw 2.203 2.520 nonbonded pdb=" NH1 ARG A 636 " pdb=" O THR A 683 " model vdw 2.260 2.520 ... (remaining 44653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.090 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.002 0.021 5779 Z= 0.163 Angle : 0.506 6.490 7795 Z= 0.265 Chirality : 0.043 0.156 846 Planarity : 0.004 0.052 1012 Dihedral : 15.709 176.438 2203 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.31), residues: 716 helix: 0.91 (0.39), residues: 193 sheet: -1.35 (0.40), residues: 196 loop : -1.26 (0.31), residues: 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.681 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1845 time to fit residues: 34.3850 Evaluate side-chains 120 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5779 Z= 0.208 Angle : 0.532 6.681 7795 Z= 0.276 Chirality : 0.045 0.134 846 Planarity : 0.004 0.053 1012 Dihedral : 10.505 175.553 787 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.79 % Allowed : 12.23 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.32), residues: 716 helix: 1.20 (0.37), residues: 211 sheet: -1.26 (0.42), residues: 177 loop : -1.64 (0.31), residues: 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.646 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.2084 time to fit residues: 36.1700 Evaluate side-chains 130 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0586 time to fit residues: 1.6483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5779 Z= 0.215 Angle : 0.518 6.809 7795 Z= 0.266 Chirality : 0.044 0.130 846 Planarity : 0.004 0.054 1012 Dihedral : 10.499 174.489 787 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.96 % Allowed : 14.68 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.32), residues: 716 helix: 1.25 (0.37), residues: 212 sheet: -1.40 (0.38), residues: 200 loop : -1.41 (0.33), residues: 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.694 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 145 average time/residue: 0.2048 time to fit residues: 37.5901 Evaluate side-chains 128 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1203 time to fit residues: 1.5442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5779 Z= 0.157 Angle : 0.485 6.379 7795 Z= 0.250 Chirality : 0.043 0.132 846 Planarity : 0.004 0.051 1012 Dihedral : 10.434 176.768 787 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 16.31 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.32), residues: 716 helix: 1.48 (0.38), residues: 213 sheet: -1.21 (0.38), residues: 197 loop : -1.35 (0.33), residues: 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.635 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 133 average time/residue: 0.1843 time to fit residues: 31.7810 Evaluate side-chains 127 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0645 time to fit residues: 1.5812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5779 Z= 0.238 Angle : 0.539 9.017 7795 Z= 0.273 Chirality : 0.044 0.134 846 Planarity : 0.004 0.054 1012 Dihedral : 10.440 174.093 787 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.45 % Allowed : 19.58 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 716 helix: 1.44 (0.37), residues: 213 sheet: -1.44 (0.37), residues: 204 loop : -1.39 (0.34), residues: 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.659 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 134 average time/residue: 0.1916 time to fit residues: 33.1000 Evaluate side-chains 129 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0653 time to fit residues: 1.6132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5779 Z= 0.249 Angle : 0.543 7.818 7795 Z= 0.278 Chirality : 0.044 0.130 846 Planarity : 0.004 0.054 1012 Dihedral : 10.486 174.014 787 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.77 % Allowed : 20.07 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.32), residues: 716 helix: 1.39 (0.37), residues: 213 sheet: -1.48 (0.37), residues: 204 loop : -1.42 (0.34), residues: 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 0.642 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 131 average time/residue: 0.1923 time to fit residues: 32.4499 Evaluate side-chains 128 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0596 time to fit residues: 1.7791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 41 optimal weight: 0.6980 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5779 Z= 0.145 Angle : 0.508 7.498 7795 Z= 0.256 Chirality : 0.043 0.133 846 Planarity : 0.004 0.047 1012 Dihedral : 10.412 177.253 787 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.63 % Allowed : 20.88 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.32), residues: 716 helix: 1.57 (0.37), residues: 213 sheet: -1.16 (0.38), residues: 196 loop : -1.33 (0.33), residues: 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.681 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 129 average time/residue: 0.1841 time to fit residues: 30.9954 Evaluate side-chains 120 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0548 time to fit residues: 1.0667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5779 Z= 0.300 Angle : 0.591 7.235 7795 Z= 0.303 Chirality : 0.046 0.163 846 Planarity : 0.004 0.047 1012 Dihedral : 10.497 172.746 787 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.77 % Allowed : 21.53 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.31), residues: 716 helix: 1.29 (0.37), residues: 213 sheet: -1.47 (0.37), residues: 202 loop : -1.54 (0.32), residues: 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.666 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 0.2323 time to fit residues: 40.1233 Evaluate side-chains 134 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0643 time to fit residues: 2.3326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5779 Z= 0.200 Angle : 0.548 6.807 7795 Z= 0.281 Chirality : 0.044 0.135 846 Planarity : 0.004 0.047 1012 Dihedral : 10.544 177.750 787 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.98 % Allowed : 22.02 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.32), residues: 716 helix: 1.41 (0.37), residues: 213 sheet: -1.48 (0.37), residues: 204 loop : -1.48 (0.32), residues: 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.649 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 123 average time/residue: 0.2022 time to fit residues: 31.9031 Evaluate side-chains 122 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0576 time to fit residues: 1.2546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5779 Z= 0.241 Angle : 0.568 6.844 7795 Z= 0.291 Chirality : 0.044 0.136 846 Planarity : 0.004 0.047 1012 Dihedral : 10.567 178.266 787 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.33 % Allowed : 23.49 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.31), residues: 716 helix: 1.27 (0.37), residues: 213 sheet: -1.51 (0.37), residues: 204 loop : -1.54 (0.32), residues: 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.682 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 120 average time/residue: 0.2109 time to fit residues: 32.3902 Evaluate side-chains 118 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0585 time to fit residues: 1.0473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** 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 = 0.3832 r_free = 0.3832 target = 0.177473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.144027 restraints weight = 7039.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147464 restraints weight = 3999.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.149807 restraints weight = 2714.510| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5779 Z= 0.197 Angle : 0.553 6.663 7795 Z= 0.283 Chirality : 0.044 0.132 846 Planarity : 0.004 0.048 1012 Dihedral : 10.524 178.104 787 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.65 % Allowed : 23.65 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.31), residues: 716 helix: 1.36 (0.38), residues: 213 sheet: -1.50 (0.37), residues: 200 loop : -1.45 (0.32), residues: 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1541.14 seconds wall clock time: 28 minutes 34.70 seconds (1714.70 seconds total)