Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 05:27:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/07_2023/8etm_28594_updated.pdb" } resolution = 3.2 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 4524 2.51 5 N 1138 2.21 5 O 1090 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 6800 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.55 Number of scatterers: 6800 At special positions: 0 Unit cell: (112.88, 98.77, 83, 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 42 16.00 F 6 9.00 O 1090 8.00 N 1138 7.00 C 4524 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 0 sheets defined 70.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 88 through 111 removed outlier: 5.575A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 132 through 156 removed outlier: 4.316A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 191 through 227 removed outlier: 3.612A pdb=" N SER A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 275 through 305 removed outlier: 4.439A pdb=" N VAL A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.885A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.435A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.797A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 111 removed outlier: 5.575A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 132 through 156 removed outlier: 4.315A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 184 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 191 through 227 removed outlier: 3.612A pdb=" N SER B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 275 through 305 removed outlier: 4.440A pdb=" N VAL B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.885A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 371 through 374 No H-bonds generated for 'chain 'B' and resid 371 through 374' Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 395 Processing helix chain 'B' and resid 400 through 419 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 429 through 447 removed outlier: 4.434A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.798A pdb=" N LEU B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1140 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: 1.78 Time building geometry restraints manager: 3.13 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: 1938 1.33 - 1.45: 1357 1.45 - 1.57: 3659 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 7022 Sorted by residual: bond pdb=" C14 WTT A 501 " pdb=" N1 WTT A 501 " ideal model delta sigma weight residual 1.476 1.331 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C14 WTT B 501 " pdb=" N1 WTT B 501 " ideal model delta sigma weight residual 1.476 1.331 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C10 WTT B 501 " pdb=" C9 WTT B 501 " ideal model delta sigma weight residual 1.561 1.475 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C10 WTT A 501 " pdb=" C9 WTT A 501 " ideal model delta sigma weight residual 1.561 1.475 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C20 WTT B 501 " pdb=" O1 WTT B 501 " ideal model delta sigma weight residual 1.412 1.333 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 7017 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.32: 190 106.32 - 113.24: 3760 113.24 - 120.16: 2765 120.16 - 127.09: 2721 127.09 - 134.01: 126 Bond angle restraints: 9562 Sorted by residual: angle pdb=" N GLY A 464 " pdb=" CA GLY A 464 " pdb=" C GLY A 464 " ideal model delta sigma weight residual 113.18 121.08 -7.90 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY B 464 " pdb=" CA GLY B 464 " pdb=" C GLY B 464 " ideal model delta sigma weight residual 113.18 121.05 -7.87 2.37e+00 1.78e-01 1.10e+01 angle pdb=" C PHE B 342 " pdb=" N HIS B 343 " pdb=" CA HIS B 343 " ideal model delta sigma weight residual 122.42 116.69 5.73 1.77e+00 3.19e-01 1.05e+01 angle pdb=" C PHE A 342 " pdb=" N HIS A 343 " pdb=" CA HIS A 343 " ideal model delta sigma weight residual 122.42 116.70 5.72 1.77e+00 3.19e-01 1.04e+01 angle pdb=" C ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta sigma weight residual 113.70 110.75 2.95 9.50e-01 1.11e+00 9.63e+00 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3556 17.85 - 35.70: 392 35.70 - 53.55: 63 53.55 - 71.39: 8 71.39 - 89.24: 7 Dihedral angle restraints: 4026 sinusoidal: 1614 harmonic: 2412 Sorted by residual: dihedral pdb=" CA ILE B 463 " pdb=" C ILE B 463 " pdb=" N GLY B 464 " pdb=" CA GLY B 464 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 4023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 1031 1.025 - 2.051: 0 2.051 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.127: 1 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C5 WTT B 501 " pdb=" C28 WTT B 501 " pdb=" C4 WTT B 501 " pdb=" C6 WTT B 501 " both_signs ideal model delta sigma weight residual False -2.74 2.38 -5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" C5 WTT A 501 " pdb=" C28 WTT A 501 " pdb=" C4 WTT A 501 " pdb=" C6 WTT A 501 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2 WTT A 501 " pdb=" C1 WTT A 501 " pdb=" C29 WTT A 501 " pdb=" C3 WTT A 501 " both_signs ideal model delta sigma weight residual False 2.73 2.58 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1029 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 WTT B 501 " -0.090 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C14 WTT B 501 " 0.082 2.00e-02 2.50e+03 pdb=" C15 WTT B 501 " -0.350 2.00e-02 2.50e+03 pdb=" N1 WTT B 501 " 0.537 2.00e-02 2.50e+03 pdb=" O2 WTT B 501 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WTT B 501 " -0.114 2.00e-02 2.50e+03 1.65e-01 7.45e+02 pdb=" C10 WTT B 501 " 0.025 2.00e-02 2.50e+03 pdb=" C11 WTT B 501 " -0.073 2.00e-02 2.50e+03 pdb=" C12 WTT B 501 " -0.171 2.00e-02 2.50e+03 pdb=" C13 WTT B 501 " -0.158 2.00e-02 2.50e+03 pdb=" C14 WTT B 501 " 0.419 2.00e-02 2.50e+03 pdb=" C23 WTT B 501 " -0.072 2.00e-02 2.50e+03 pdb=" C24 WTT B 501 " 0.013 2.00e-02 2.50e+03 pdb=" C25 WTT B 501 " 0.058 2.00e-02 2.50e+03 pdb=" C9 WTT B 501 " 0.175 2.00e-02 2.50e+03 pdb=" N2 WTT B 501 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 WTT A 501 " -0.161 2.00e-02 2.50e+03 1.86e-01 4.35e+02 pdb=" C14 WTT A 501 " 0.062 2.00e-02 2.50e+03 pdb=" C15 WTT A 501 " -0.223 2.00e-02 2.50e+03 pdb=" N1 WTT A 501 " 0.307 2.00e-02 2.50e+03 pdb=" O2 WTT A 501 " 0.016 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1497 2.76 - 3.30: 7110 3.30 - 3.83: 11454 3.83 - 4.37: 12928 4.37 - 4.90: 22338 Nonbonded interactions: 55327 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.226 2.520 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.226 2.520 nonbonded pdb=" O TYR B 372 " pdb=" ND2 ASN B 376 " model vdw 2.249 2.520 nonbonded pdb=" O TYR A 372 " pdb=" ND2 ASN A 376 " model vdw 2.249 2.520 nonbonded pdb=" ND2 ASN B 378 " pdb=" O2 WTT B 501 " model vdw 2.252 2.520 ... (remaining 55322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 0.600 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: 4.100 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 21.310 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.009 0.145 7022 Z= 0.624 Angle : 0.845 8.373 9562 Z= 0.423 Chirality : 0.166 5.127 1032 Planarity : 0.013 0.302 1170 Dihedral : 14.880 89.242 2462 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer Outliers : 0.00 % 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: -3.61 (0.24), residues: 804 helix: -1.46 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -4.91 (0.29), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.854 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2585 time to fit residues: 47.6876 Evaluate side-chains 104 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 201 HIS ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 201 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7022 Z= 0.217 Angle : 0.751 13.664 9562 Z= 0.334 Chirality : 0.040 0.225 1032 Planarity : 0.004 0.033 1170 Dihedral : 7.304 81.240 918 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.82 % 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: -1.01 (0.30), residues: 804 helix: 0.37 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.88 (0.40), residues: 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.783 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 132 average time/residue: 0.2087 time to fit residues: 35.8841 Evaluate side-chains 112 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0657 time to fit residues: 2.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.0020 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 141 ASN A 292 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN B 107 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7022 Z= 0.191 Angle : 0.669 14.101 9562 Z= 0.308 Chirality : 0.042 0.202 1032 Planarity : 0.004 0.032 1170 Dihedral : 6.910 80.755 918 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 1.54 % 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: -0.04 (0.31), residues: 804 helix: 1.13 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.60 (0.39), residues: 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.704 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 130 average time/residue: 0.2251 time to fit residues: 37.5542 Evaluate side-chains 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0637 time to fit residues: 1.8107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 7022 Z= 0.345 Angle : 0.781 11.705 9562 Z= 0.365 Chirality : 0.046 0.290 1032 Planarity : 0.005 0.037 1170 Dihedral : 7.382 87.164 918 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer Outliers : 2.24 % 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: -0.21 (0.31), residues: 804 helix: 1.00 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.68 (0.37), residues: 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.836 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.2207 time to fit residues: 39.6947 Evaluate side-chains 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0683 time to fit residues: 2.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7022 Z= 0.240 Angle : 0.703 11.327 9562 Z= 0.321 Chirality : 0.041 0.180 1032 Planarity : 0.004 0.033 1170 Dihedral : 7.053 83.268 918 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 1.40 % 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: 0.16 (0.31), residues: 804 helix: 1.24 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -3.54 (0.38), residues: 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.914 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 130 average time/residue: 0.2283 time to fit residues: 38.2802 Evaluate side-chains 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0676 time to fit residues: 1.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 0.0020 chunk 74 optimal weight: 4.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 7022 Z= 0.149 Angle : 0.669 12.973 9562 Z= 0.301 Chirality : 0.039 0.145 1032 Planarity : 0.004 0.033 1170 Dihedral : 6.683 75.869 918 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 1.12 % 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: 0.65 (0.32), residues: 804 helix: 1.63 (0.23), residues: 604 sheet: None (None), residues: 0 loop : -3.51 (0.37), residues: 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.782 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 111 average time/residue: 0.2487 time to fit residues: 35.1430 Evaluate side-chains 111 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1412 time to fit residues: 2.6547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7022 Z= 0.225 Angle : 0.689 11.919 9562 Z= 0.314 Chirality : 0.041 0.169 1032 Planarity : 0.004 0.035 1170 Dihedral : 6.724 65.771 918 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.84 % 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: 0.59 (0.32), residues: 804 helix: 1.56 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.46 (0.37), residues: 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.941 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 115 average time/residue: 0.2562 time to fit residues: 37.6879 Evaluate side-chains 111 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.864 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0674 time to fit residues: 1.1781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7022 Z= 0.238 Angle : 0.690 12.046 9562 Z= 0.314 Chirality : 0.041 0.205 1032 Planarity : 0.004 0.034 1170 Dihedral : 6.714 68.450 918 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.42 % 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: 0.58 (0.32), residues: 804 helix: 1.59 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.49 (0.37), residues: 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.779 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 114 average time/residue: 0.2468 time to fit residues: 35.6111 Evaluate side-chains 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0735 time to fit residues: 1.3413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7022 Z= 0.213 Angle : 0.679 12.404 9562 Z= 0.311 Chirality : 0.041 0.190 1032 Planarity : 0.004 0.034 1170 Dihedral : 6.648 69.888 918 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.42 % 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: 0.58 (0.31), residues: 804 helix: 1.59 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.48 (0.37), residues: 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.821 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 116 average time/residue: 0.2647 time to fit residues: 39.1448 Evaluate side-chains 116 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1676 time to fit residues: 1.7730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 49 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7022 Z= 0.219 Angle : 0.688 12.047 9562 Z= 0.314 Chirality : 0.041 0.166 1032 Planarity : 0.004 0.034 1170 Dihedral : 6.725 74.881 918 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.14 % 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: 0.65 (0.31), residues: 804 helix: 1.63 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.40 (0.36), residues: 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.776 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.2433 time to fit residues: 34.1678 Evaluate side-chains 108 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0907 time to fit residues: 1.1141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125384 restraints weight = 9614.771| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.05 r_work: 0.3385 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 7022 Z= 0.189 Angle : 0.692 12.096 9562 Z= 0.313 Chirality : 0.041 0.164 1032 Planarity : 0.004 0.034 1170 Dihedral : 6.703 77.500 918 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.28 % 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: 804 helix: 1.61 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.45 (0.37), residues: 200 =============================================================================== Job complete usr+sys time: 1721.67 seconds wall clock time: 32 minutes 6.85 seconds (1926.85 seconds total)