Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:57:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/04_2023/8ej5_28176.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3712 2.51 5 N 981 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3556 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 3.54, per 1000 atoms: 0.61 Number of scatterers: 5818 At special positions: 0 Unit cell: (74.368, 95.616, 131.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 1108 8.00 N 981 7.00 C 3712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 804.2 milliseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 59.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.300A pdb=" N GLY A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.151A pdb=" N TRP A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 353 through 367 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.662A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.824A pdb=" N GLN B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.529A pdb=" N TYR B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 86 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.825A pdb=" N GLN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.526A pdb=" N TYR C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.806A pdb=" N GLN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 45 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.527A pdb=" N TYR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 255 removed outlier: 6.199A pdb=" N THR A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 317 removed outlier: 5.139A pdb=" N GLY A 315 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 454 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 434 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 422 " --> pdb=" O PHE A 404 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 906 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: 1.50 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1171 1.32 - 1.45: 1552 1.45 - 1.57: 3214 1.57 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5966 Sorted by residual: bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta sigma weight residual 1.462 1.492 -0.031 8.70e-03 1.32e+04 1.23e+01 bond pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N GLU D 47 " pdb=" CA GLU D 47 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.07e+01 ... (remaining 5961 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.55: 171 106.55 - 113.78: 3065 113.78 - 121.02: 2861 121.02 - 128.26: 1954 128.26 - 135.49: 49 Bond angle restraints: 8100 Sorted by residual: angle pdb=" CA GLY A 314 " pdb=" C GLY A 314 " pdb=" N GLY A 315 " ideal model delta sigma weight residual 115.11 120.97 -5.86 9.50e-01 1.11e+00 3.81e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.56 118.63 -8.07 1.36e+00 5.41e-01 3.52e+01 angle pdb=" N ASN A 284 " pdb=" CA ASN A 284 " pdb=" C ASN A 284 " ideal model delta sigma weight residual 111.54 104.26 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" N LYS A 272 " pdb=" CA LYS A 272 " pdb=" C LYS A 272 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" CA LYS A 242 " pdb=" C LYS A 242 " pdb=" O LYS A 242 " ideal model delta sigma weight residual 120.63 114.92 5.71 1.08e+00 8.57e-01 2.80e+01 ... (remaining 8095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3161 16.49 - 32.97: 214 32.97 - 49.46: 63 49.46 - 65.95: 11 65.95 - 82.44: 3 Dihedral angle restraints: 3452 sinusoidal: 1360 harmonic: 2092 Sorted by residual: dihedral pdb=" C ASN A 316 " pdb=" N ASN A 316 " pdb=" CA ASN A 316 " pdb=" CB ASN A 316 " ideal model delta harmonic sigma weight residual -122.60 -133.15 10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" CB ASN A 465 " pdb=" CG ASN A 465 " ideal model delta sinusoidal sigma weight residual -180.00 -125.56 -54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ILE A 275 " pdb=" CB ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CD1 ILE A 275 " ideal model delta sinusoidal sigma weight residual -180.00 -127.13 -52.87 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 3449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 366 0.067 - 0.135: 376 0.135 - 0.202: 85 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN A 316 " pdb=" N ASN A 316 " pdb=" C ASN A 316 " pdb=" CB ASN A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 832 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 84 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 84 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 84 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 85 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 78 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR D 78 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 78 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 78 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 78 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " 0.042 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B 78 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.019 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2740 2.96 - 3.44: 6379 3.44 - 3.93: 10549 3.93 - 4.41: 11549 4.41 - 4.90: 18520 Nonbonded interactions: 49737 Sorted by model distance: nonbonded pdb=" O SER A 84 " pdb=" OE1 GLU B 58 " model vdw 2.472 3.040 nonbonded pdb=" O ARG A 311 " pdb=" N ASP A 456 " model vdw 2.478 2.520 nonbonded pdb=" N PHE A 244 " pdb=" O ILE A 251 " model vdw 2.487 2.520 nonbonded pdb=" O GLY A 281 " pdb=" OD1 ASP A 464 " model vdw 2.488 3.040 nonbonded pdb=" N THR A 318 " pdb=" OD1 ASN A 321 " model vdw 2.490 2.520 ... (remaining 49732 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 4.060 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.012 0.047 5966 Z= 0.776 Angle : 1.519 9.118 8100 Z= 1.153 Chirality : 0.090 0.337 835 Planarity : 0.010 0.109 1071 Dihedral : 12.691 82.437 2124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.33 % 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: 1.40 (0.30), residues: 717 helix: 1.44 (0.25), residues: 397 sheet: 0.11 (0.71), residues: 42 loop : 0.49 (0.38), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 333 average time/residue: 0.1941 time to fit residues: 81.4385 Evaluate side-chains 185 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0622 time to fit residues: 1.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN C 20 GLN C 32 ASN C 83 ASN D 32 ASN D 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5966 Z= 0.211 Angle : 0.657 10.011 8100 Z= 0.346 Chirality : 0.044 0.237 835 Planarity : 0.006 0.142 1071 Dihedral : 5.906 88.696 784 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.95 % Favored : 97.77 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.64 (0.32), residues: 717 helix: 1.72 (0.26), residues: 403 sheet: 0.69 (0.73), residues: 44 loop : 0.30 (0.39), residues: 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.1652 time to fit residues: 50.6517 Evaluate side-chains 176 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5966 Z= 0.183 Angle : 0.608 9.623 8100 Z= 0.318 Chirality : 0.042 0.203 835 Planarity : 0.004 0.042 1071 Dihedral : 5.549 74.282 784 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.81 % Favored : 97.91 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.59 (0.32), residues: 717 helix: 1.69 (0.26), residues: 402 sheet: 0.90 (0.74), residues: 43 loop : 0.22 (0.39), residues: 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.1611 time to fit residues: 49.2184 Evaluate side-chains 180 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0894 time to fit residues: 1.0919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 14 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 5966 Z= 0.281 Angle : 0.729 10.399 8100 Z= 0.384 Chirality : 0.044 0.188 835 Planarity : 0.004 0.036 1071 Dihedral : 6.496 84.444 784 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.65 % Favored : 97.07 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.92 (0.31), residues: 717 helix: 1.11 (0.26), residues: 406 sheet: 0.73 (0.71), residues: 44 loop : -0.05 (0.39), residues: 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1594 time to fit residues: 47.5177 Evaluate side-chains 173 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 409 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5966 Z= 0.183 Angle : 0.632 9.674 8100 Z= 0.327 Chirality : 0.042 0.192 835 Planarity : 0.003 0.036 1071 Dihedral : 5.958 80.745 784 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.37 % Favored : 97.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.90 (0.31), residues: 717 helix: 1.11 (0.26), residues: 399 sheet: 1.16 (0.71), residues: 42 loop : -0.14 (0.39), residues: 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1518 time to fit residues: 44.0131 Evaluate side-chains 175 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 54 ASN ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.8487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5966 Z= 0.239 Angle : 0.667 8.990 8100 Z= 0.350 Chirality : 0.043 0.191 835 Planarity : 0.004 0.038 1071 Dihedral : 6.371 82.565 784 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.35 % Favored : 96.37 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.50 (0.31), residues: 717 helix: 0.84 (0.25), residues: 408 sheet: 0.92 (0.75), residues: 44 loop : -0.46 (0.39), residues: 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1602 time to fit residues: 46.1585 Evaluate side-chains 167 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 33 ASN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.8841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5966 Z= 0.182 Angle : 0.661 9.328 8100 Z= 0.342 Chirality : 0.043 0.193 835 Planarity : 0.004 0.038 1071 Dihedral : 6.186 84.641 784 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.35 % Favored : 96.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.31), residues: 717 helix: 0.80 (0.25), residues: 408 sheet: 0.81 (0.75), residues: 44 loop : -0.46 (0.38), residues: 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1650 time to fit residues: 48.3600 Evaluate side-chains 169 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.9141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5966 Z= 0.182 Angle : 0.652 8.463 8100 Z= 0.346 Chirality : 0.044 0.188 835 Planarity : 0.004 0.038 1071 Dihedral : 6.235 87.545 784 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.49 % Favored : 96.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 717 helix: 0.67 (0.25), residues: 406 sheet: 0.85 (0.77), residues: 44 loop : -0.56 (0.38), residues: 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1809 time to fit residues: 49.8472 Evaluate side-chains 166 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.9403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5966 Z= 0.167 Angle : 0.686 9.841 8100 Z= 0.354 Chirality : 0.045 0.190 835 Planarity : 0.004 0.038 1071 Dihedral : 6.210 89.969 784 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.49 % Favored : 96.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.31), residues: 717 helix: 0.53 (0.25), residues: 407 sheet: 0.68 (0.75), residues: 44 loop : -0.59 (0.38), residues: 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1570 time to fit residues: 44.7636 Evaluate side-chains 163 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 33 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 17 ASN C 33 ASN D 30 ASN D 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.9732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 5966 Z= 0.232 Angle : 0.725 8.773 8100 Z= 0.385 Chirality : 0.045 0.225 835 Planarity : 0.004 0.039 1071 Dihedral : 6.343 86.081 784 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.63 % Favored : 96.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.30), residues: 717 helix: 0.27 (0.25), residues: 408 sheet: 0.72 (0.77), residues: 44 loop : -0.70 (0.37), residues: 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1586 time to fit residues: 41.8389 Evaluate side-chains 160 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN B 20 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 40 GLN D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071658 restraints weight = 25090.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074043 restraints weight = 14866.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075648 restraints weight = 9813.765| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.9976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 5966 Z= 0.185 Angle : 0.691 8.004 8100 Z= 0.367 Chirality : 0.045 0.200 835 Planarity : 0.004 0.039 1071 Dihedral : 6.097 84.453 784 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.18 % Favored : 95.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.30), residues: 717 helix: 0.28 (0.25), residues: 401 sheet: 0.68 (0.74), residues: 44 loop : -0.59 (0.37), residues: 272 =============================================================================== Job complete usr+sys time: 1571.82 seconds wall clock time: 29 minutes 10.28 seconds (1750.28 seconds total)