Starting phenix.real_space_refine on Tue Nov 14 01:36:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_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_28594/11_2023/8etm_28594_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etm_28594/11_2023/8etm_28594_updated.pdb" } resolution = 3.2 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= 0.000 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 4.05, per 1000 atoms: 0.60 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 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: 1.39 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: 1.76 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 - 23.98: 3795 23.98 - 47.96: 213 47.96 - 71.94: 20 71.94 - 95.92: 9 95.92 - 119.90: 1 Dihedral angle restraints: 4038 sinusoidal: 1626 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 4035 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.420 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- 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 : 15.266 119.900 2474 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 % Allowed : 6.44 % Favored : 93.56 % 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 : 0.847 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2616 time to fit residues: 48.3500 Evaluate side-chains 104 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0028 ------------------------------------------------------------------------------- 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 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 B 306 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7022 Z= 0.216 Angle : 0.748 12.880 9562 Z= 0.334 Chirality : 0.040 0.123 1032 Planarity : 0.004 0.033 1170 Dihedral : 9.454 101.401 930 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.96 % Allowed : 13.31 % Favored : 84.73 % 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: -0.93 (0.30), residues: 804 helix: 0.43 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.85 (0.41), 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 135 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.682 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.2181 time to fit residues: 37.3135 Evaluate side-chains 112 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0656 time to fit residues: 2.4970 ------------------------------------------------------------------------------- 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: 0.1980 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 71 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7022 Z= 0.149 Angle : 0.651 13.829 9562 Z= 0.295 Chirality : 0.040 0.209 1032 Planarity : 0.003 0.032 1170 Dihedral : 9.107 94.581 930 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.12 % Allowed : 15.55 % Favored : 83.33 % 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: -0.03 (0.31), residues: 804 helix: 1.15 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -3.62 (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 119 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.735 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 118 average time/residue: 0.2207 time to fit residues: 33.8101 Evaluate side-chains 104 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0657 time to fit residues: 1.7316 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** A 474 HIS B 119 GLN B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7022 Z= 0.188 Angle : 0.664 10.639 9562 Z= 0.306 Chirality : 0.042 0.210 1032 Planarity : 0.004 0.031 1170 Dihedral : 9.084 99.421 930 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.40 % Allowed : 16.11 % Favored : 82.49 % 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: 0.32 (0.32), residues: 804 helix: 1.36 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.58 (0.40), residues: 198 *********************** 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 136 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.680 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.2569 time to fit residues: 42.1877 Evaluate side-chains 107 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0600 time to fit residues: 1.7158 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 292 GLN ** A 366 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7022 Z= 0.274 Angle : 0.742 14.089 9562 Z= 0.342 Chirality : 0.045 0.264 1032 Planarity : 0.005 0.044 1170 Dihedral : 9.307 106.556 930 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.38 % Allowed : 16.81 % Favored : 80.81 % 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: 0.28 (0.31), residues: 804 helix: 1.27 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.42 (0.40), residues: 196 *********************** 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 147 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.752 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 141 average time/residue: 0.2399 time to fit residues: 43.0826 Evaluate side-chains 115 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0680 time to fit residues: 1.9251 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 69 HIS B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7022 Z= 0.262 Angle : 0.730 11.256 9562 Z= 0.332 Chirality : 0.043 0.196 1032 Planarity : 0.004 0.032 1170 Dihedral : 9.129 101.691 930 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.84 % Allowed : 19.61 % Favored : 79.55 % 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: 0.44 (0.32), residues: 804 helix: 1.43 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.43 (0.38), 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 123 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.833 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 118 average time/residue: 0.2267 time to fit residues: 34.4689 Evaluate side-chains 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0714 time to fit residues: 1.3622 ------------------------------------------------------------------------------- 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: 6.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 354 GLN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 292 GLN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7022 Z= 0.364 Angle : 0.787 11.569 9562 Z= 0.365 Chirality : 0.046 0.230 1032 Planarity : 0.005 0.035 1170 Dihedral : 9.544 111.091 930 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.68 % Allowed : 20.17 % Favored : 78.15 % 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: -0.01 (0.31), residues: 804 helix: 1.09 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.58 (0.37), residues: 198 *********************** 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 132 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.771 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 126 average time/residue: 0.2347 time to fit residues: 37.8957 Evaluate side-chains 116 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0761 time to fit residues: 1.6788 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7022 Z= 0.309 Angle : 0.749 11.705 9562 Z= 0.342 Chirality : 0.043 0.213 1032 Planarity : 0.005 0.038 1170 Dihedral : 9.389 104.432 930 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.98 % Allowed : 21.85 % Favored : 77.17 % 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: 0.17 (0.31), residues: 804 helix: 1.23 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.56 (0.36), residues: 198 *********************** 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 119 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.840 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.2386 time to fit residues: 35.5193 Evaluate side-chains 113 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0601 time to fit residues: 1.4339 ------------------------------------------------------------------------------- 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: 0.2980 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7022 Z= 0.171 Angle : 0.696 11.607 9562 Z= 0.313 Chirality : 0.041 0.195 1032 Planarity : 0.004 0.036 1170 Dihedral : 9.101 97.247 930 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.14 % Allowed : 22.83 % Favored : 77.03 % 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: 0.60 (0.32), residues: 804 helix: 1.55 (0.23), residues: 606 sheet: None (None), residues: 0 loop : -3.45 (0.36), residues: 198 *********************** 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 114 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.732 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2297 time to fit residues: 33.6921 Evaluate side-chains 106 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0675 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7022 Z= 0.448 Angle : 0.828 11.419 9562 Z= 0.384 Chirality : 0.047 0.238 1032 Planarity : 0.005 0.035 1170 Dihedral : 9.665 111.388 930 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.84 % Allowed : 22.83 % Favored : 76.33 % 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: 0.09 (0.31), residues: 804 helix: 1.11 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.41 (0.37), residues: 196 ********************** 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 113 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.887 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 110 average time/residue: 0.2606 time to fit residues: 36.4251 Evaluate side-chains 102 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0802 time to fit residues: 1.5659 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121979 restraints weight = 9335.374| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.15 r_work: 0.3336 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.7591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7022 Z= 0.183 Angle : 0.742 12.030 9562 Z= 0.332 Chirality : 0.041 0.192 1032 Planarity : 0.004 0.037 1170 Dihedral : 9.228 99.812 930 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.28 % Allowed : 22.69 % Favored : 77.03 % 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: 0.46 (0.31), residues: 804 helix: 1.40 (0.23), residues: 608 sheet: None (None), residues: 0 loop : -3.37 (0.36), residues: 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.85 seconds wall clock time: 31 minutes 29.01 seconds (1889.01 seconds total)