Starting phenix.real_space_refine (version: dev) on Mon Dec 12 07:11:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2022/7kxy_23067.pdb" } resolution = 4.4 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 68": "OD1" <-> "OD2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 501": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "B ARG 1551": "NH1" <-> "NH2" Residue "B TYR 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1603": "NH1" <-> "NH2" Residue "B ARG 1606": "NH1" <-> "NH2" Residue "B ARG 1631": "NH1" <-> "NH2" Residue "B TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1659": "OE1" <-> "OE2" Residue "B PHE 1666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1698": "NH1" <-> "NH2" Residue "B TYR 1702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1761": "NH1" <-> "NH2" Residue "B TYR 1793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1799": "NH1" <-> "NH2" Residue "B PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1862": "OE1" <-> "OE2" Residue "B ARG 1865": "NH1" <-> "NH2" Residue "B ARG 1877": "NH1" <-> "NH2" Residue "B ARG 1880": "NH1" <-> "NH2" Residue "B ARG 1907": "NH1" <-> "NH2" Residue "B PHE 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1985": "NH1" <-> "NH2" Residue "B TYR 1989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2001": "OE1" <-> "OE2" Residue "B TYR 2012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2019": "NH1" <-> "NH2" Residue "B ARG 2072": "NH1" <-> "NH2" Residue "B ARG 2080": "NH1" <-> "NH2" Residue "B TYR 2121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2140": "NH1" <-> "NH2" Residue "B ARG 2171": "NH1" <-> "NH2" Residue "B PHE 2191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9510 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4704 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 30, 'TRANS': 557} Chain breaks: 8 Chain: "B" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4806 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 564} Chain breaks: 4 Time building chain proxies: 5.92, per 1000 atoms: 0.62 Number of scatterers: 9510 At special positions: 0 Unit cell: (85.8, 96.8, 134.2, 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 48 16.00 O 1784 8.00 N 1630 7.00 C 6048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B1697 " - pdb=" SG CYS B1723 " distance=2.03 Simple disulfide: pdb=" SG CYS B1879 " - pdb=" SG CYS B2033 " distance=2.03 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 12 sheets defined 2.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 640 through 645 removed outlier: 4.331A pdb=" N LYS A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 1779 through 1783 removed outlier: 3.698A pdb=" N MET B1783 " --> pdb=" O ILE B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1861 through 1866 removed outlier: 3.506A pdb=" N GLN B1864 " --> pdb=" O GLY B1861 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B1865 " --> pdb=" O GLU B1862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.980A pdb=" N ALA A 9 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.969A pdb=" N LEU A 62 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS A 165 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 164 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.584A pdb=" N ILE A 225 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 268 " --> pdb=" O TRP A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 334 removed outlier: 3.869A pdb=" N VAL A 331 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.741A pdb=" N LEU A 494 " --> pdb=" O ILE A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 594 through 595 removed outlier: 3.585A pdb=" N LEU A 594 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1555 through 1556 Processing sheet with id=AA8, first strand: chain 'B' and resid 1620 through 1622 removed outlier: 3.506A pdb=" N LEU B1721 " --> pdb=" O ILE B1620 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B1622 " --> pdb=" O LEU B1721 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1800 through 1801 Processing sheet with id=AB1, first strand: chain 'B' and resid 1814 through 1816 removed outlier: 3.744A pdb=" N HIS B1815 " --> pdb=" O ASN B1857 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B1857 " --> pdb=" O HIS B1815 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1896 through 1897 removed outlier: 4.499A pdb=" N LYS B1896 " --> pdb=" O GLN B1936 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B1936 " --> pdb=" O LYS B1896 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 1977 through 1978 42 hydrogen bonds defined for protein. 90 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: 2.32 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3065 1.35 - 1.47: 2405 1.47 - 1.59: 4197 1.59 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 9746 Sorted by residual: bond pdb=" C ILE B2176 " pdb=" N PRO B2177 " ideal model delta sigma weight residual 1.335 1.356 -0.021 8.70e-03 1.32e+04 5.81e+00 bond pdb=" CA THR B2018 " pdb=" C THR B2018 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.30e-03 2.52e+04 3.00e+00 bond pdb=" CA ARG B2074 " pdb=" CB ARG B2074 " ideal model delta sigma weight residual 1.528 1.557 -0.029 1.67e-02 3.59e+03 2.95e+00 bond pdb=" C GLU A 42 " pdb=" N PRO A 43 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.33e-02 5.65e+03 2.32e+00 bond pdb=" CA PHE B1872 " pdb=" CB PHE B1872 " ideal model delta sigma weight residual 1.526 1.549 -0.022 1.53e-02 4.27e+03 2.16e+00 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.47: 321 106.47 - 113.37: 5167 113.37 - 120.26: 3342 120.26 - 127.16: 4215 127.16 - 134.06: 139 Bond angle restraints: 13184 Sorted by residual: angle pdb=" CA THR B2018 " pdb=" C THR B2018 " pdb=" N ARG B2019 " ideal model delta sigma weight residual 119.46 116.96 2.50 6.10e-01 2.69e+00 1.68e+01 angle pdb=" C SER A 262 " pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 112.17 108.72 3.45 9.50e-01 1.11e+00 1.32e+01 angle pdb=" C TYR B1678 " pdb=" CA TYR B1678 " pdb=" CB TYR B1678 " ideal model delta sigma weight residual 114.40 109.96 4.44 1.25e+00 6.40e-01 1.26e+01 angle pdb=" CA ARG A 445 " pdb=" C ARG A 445 " pdb=" N ALA A 446 " ideal model delta sigma weight residual 118.27 123.71 -5.44 1.59e+00 3.96e-01 1.17e+01 ... (remaining 13179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5171 17.54 - 35.07: 505 35.07 - 52.61: 112 52.61 - 70.15: 24 70.15 - 87.68: 11 Dihedral angle restraints: 5823 sinusoidal: 2392 harmonic: 3431 Sorted by residual: dihedral pdb=" CA VAL A 565 " pdb=" C VAL A 565 " pdb=" N PRO A 566 " pdb=" CA PRO A 566 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA TYR A 415 " pdb=" C TYR A 415 " pdb=" N SER A 416 " pdb=" CA SER A 416 " ideal model delta harmonic sigma weight residual 180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LEU A 403 " pdb=" C LEU A 403 " pdb=" N LYS A 404 " pdb=" CA LYS A 404 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 777 0.030 - 0.060: 368 0.060 - 0.090: 165 0.090 - 0.120: 73 0.120 - 0.150: 20 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ILE B2169 " pdb=" N ILE B2169 " pdb=" C ILE B2169 " pdb=" CB ILE B2169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE B1890 " pdb=" N ILE B1890 " pdb=" C ILE B1890 " pdb=" CB ILE B1890 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1400 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 565 " 0.048 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO A 566 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 160 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO A 161 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 136 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 137 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " 0.030 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 861 2.74 - 3.28: 9626 3.28 - 3.82: 15522 3.82 - 4.36: 18165 4.36 - 4.90: 29045 Nonbonded interactions: 73219 Sorted by model distance: nonbonded pdb=" OG SER B1648 " pdb=" OG1 THR B1685 " model vdw 2.197 2.440 nonbonded pdb=" O ARG B1910 " pdb=" NH1 ARG B2027 " model vdw 2.236 2.520 nonbonded pdb=" O LYS A 607 " pdb=" OG SER B1692 " model vdw 2.260 2.440 nonbonded pdb=" O VAL B1624 " pdb=" NZ LYS B1725 " model vdw 2.276 2.520 nonbonded pdb=" OG1 THR B1962 " pdb=" O THR B2025 " model vdw 2.277 2.440 ... (remaining 73214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6048 2.51 5 N 1630 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.110 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 26.600 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 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 : 0.004 0.069 9746 Z= 0.237 Angle : 0.822 8.939 13184 Z= 0.472 Chirality : 0.046 0.150 1403 Planarity : 0.005 0.071 1689 Dihedral : 15.126 87.683 3599 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 4.16 % Allowed : 26.02 % Favored : 69.82 % Rotamer Outliers : 7.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -5.90 (0.19), residues: 1153 helix: -5.24 (0.21), residues: 25 sheet: -4.15 (0.32), residues: 174 loop : -4.26 (0.16), residues: 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 188 time to evaluate : 1.231 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: 75 outliers final: 21 residues processed: 243 average time/residue: 0.2086 time to fit residues: 71.4764 Evaluate side-chains 155 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1127 time to fit residues: 5.4852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 211 ASN A 293 GLN A 362 HIS A 448 GLN A 468 ASN A 581 GLN A 597 HIS B1547 ASN B1670 ASN B1778 HIS ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1982 ASN B1986 ASN B1991 ASN B2051 ASN B2078 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9746 Z= 0.192 Angle : 0.740 8.761 13184 Z= 0.374 Chirality : 0.048 0.189 1403 Planarity : 0.005 0.062 1689 Dihedral : 7.007 30.169 1282 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.87 % Favored : 84.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.42 (0.20), residues: 1153 helix: -4.56 (0.61), residues: 24 sheet: -3.94 (0.32), residues: 206 loop : -3.85 (0.17), residues: 923 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.137 Fit side-chains 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: 177 average time/residue: 0.2307 time to fit residues: 56.4302 Evaluate side-chains 125 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 541 ASN A 597 HIS B1713 HIS ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN B2132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9746 Z= 0.237 Angle : 0.761 8.745 13184 Z= 0.387 Chirality : 0.049 0.223 1403 Planarity : 0.006 0.060 1689 Dihedral : 7.154 28.115 1282 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 28.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 21.08 % Favored : 78.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -5.30 (0.21), residues: 1153 helix: -5.00 (0.43), residues: 31 sheet: -3.97 (0.30), residues: 230 loop : -3.66 (0.18), residues: 892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.194 Fit side-chains 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: 150 average time/residue: 0.2256 time to fit residues: 47.7119 Evaluate side-chains 114 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1553 ASN ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 9746 Z= 0.398 Angle : 0.935 10.122 13184 Z= 0.478 Chirality : 0.054 0.233 1403 Planarity : 0.007 0.066 1689 Dihedral : 8.308 31.337 1282 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 38.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 23.42 % Favored : 76.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.18 % 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: -5.52 (0.20), residues: 1153 helix: -4.84 (0.46), residues: 33 sheet: -4.20 (0.33), residues: 191 loop : -3.87 (0.17), residues: 929 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2007 time to fit residues: 40.8659 Evaluate side-chains 109 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1973 GLN ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 9746 Z= 0.302 Angle : 0.855 10.785 13184 Z= 0.432 Chirality : 0.051 0.247 1403 Planarity : 0.006 0.080 1689 Dihedral : 7.923 33.019 1282 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 34.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 22.12 % Favored : 77.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -5.47 (0.20), residues: 1153 helix: -4.80 (0.46), residues: 33 sheet: -4.17 (0.32), residues: 197 loop : -3.82 (0.17), residues: 923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2121 time to fit residues: 42.2363 Evaluate side-chains 110 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 0.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9746 Z= 0.271 Angle : 0.818 10.196 13184 Z= 0.415 Chirality : 0.050 0.231 1403 Planarity : 0.006 0.069 1689 Dihedral : 7.751 32.651 1282 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 31.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 21.25 % Favored : 78.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.09 % 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: -5.32 (0.21), residues: 1153 helix: -4.73 (0.47), residues: 33 sheet: -3.92 (0.34), residues: 190 loop : -3.76 (0.17), residues: 930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2075 time to fit residues: 42.6524 Evaluate side-chains 112 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 9746 Z= 0.382 Angle : 0.925 10.567 13184 Z= 0.471 Chirality : 0.054 0.301 1403 Planarity : 0.007 0.074 1689 Dihedral : 8.368 33.301 1282 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 39.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 25.50 % Favored : 74.33 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.18 % 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: -5.59 (0.20), residues: 1153 helix: -4.69 (0.45), residues: 33 sheet: -4.09 (0.30), residues: 219 loop : -3.92 (0.17), residues: 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.148 Fit side-chains 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: 129 average time/residue: 0.2131 time to fit residues: 40.3443 Evaluate side-chains 104 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1778 HIS ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9746 Z= 0.229 Angle : 0.799 10.061 13184 Z= 0.401 Chirality : 0.050 0.249 1403 Planarity : 0.006 0.061 1689 Dihedral : 7.470 31.994 1282 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.61 % Favored : 82.31 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % 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: -5.20 (0.21), residues: 1153 helix: -4.51 (0.53), residues: 31 sheet: -3.82 (0.33), residues: 208 loop : -3.66 (0.18), residues: 914 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.150 Fit side-chains 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: 142 average time/residue: 0.1938 time to fit residues: 40.6405 Evaluate side-chains 118 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 9746 Z= 0.305 Angle : 0.868 9.981 13184 Z= 0.437 Chirality : 0.053 0.267 1403 Planarity : 0.006 0.062 1689 Dihedral : 7.881 31.924 1282 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 33.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 23.59 % Favored : 76.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % 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: -5.35 (0.21), residues: 1153 helix: -4.58 (0.48), residues: 33 sheet: -4.00 (0.33), residues: 191 loop : -3.76 (0.17), residues: 929 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.116 Fit side-chains 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: 133 average time/residue: 0.1951 time to fit residues: 38.4587 Evaluate side-chains 110 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1729 HIS ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9746 Z= 0.248 Angle : 0.832 12.352 13184 Z= 0.414 Chirality : 0.051 0.270 1403 Planarity : 0.006 0.059 1689 Dihedral : 7.524 30.020 1282 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 28.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.78 % Favored : 82.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % 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: -5.14 (0.21), residues: 1153 helix: -4.46 (0.52), residues: 33 sheet: -3.67 (0.39), residues: 170 loop : -3.68 (0.17), residues: 950 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.143 Fit side-chains 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: 138 average time/residue: 0.2076 time to fit residues: 42.6159 Evaluate side-chains 120 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.0020 chunk 17 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.161712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.151596 restraints weight = 28472.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.153352 restraints weight = 19221.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.154611 restraints weight = 13957.188| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9746 Z= 0.212 Angle : 0.785 12.219 13184 Z= 0.387 Chirality : 0.049 0.261 1403 Planarity : 0.006 0.058 1689 Dihedral : 7.060 28.623 1282 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.39 % Favored : 81.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -4.95 (0.22), residues: 1153 helix: -4.31 (0.65), residues: 25 sheet: -3.72 (0.38), residues: 174 loop : -3.51 (0.18), residues: 954 =============================================================================== Job complete usr+sys time: 1826.76 seconds wall clock time: 34 minutes 49.28 seconds (2089.28 seconds total)