Starting phenix.real_space_refine on Thu Mar 14 18:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/03_2024/7kxy_23067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/03_2024/7kxy_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_23067/03_2024/7kxy_23067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/03_2024/7kxy_23067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/03_2024/7kxy_23067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/03_2024/7kxy_23067.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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-5265/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: 5.24, per 1000 atoms: 0.55 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 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: 0.54 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: 1.95 Time building geometry restraints manager: 3.85 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 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: 0.650 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: 3.750 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 24.890 Find NCS groups from input model: 0.240 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 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 : 19.28 Ramachandran Plot: Outliers : 4.16 % Allowed : 26.02 % Favored : 69.82 % Rotamer: Outliers : 7.18 % Allowed : 11.87 % Favored : 80.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B2094 HIS 0.003 0.001 HIS B2128 PHE 0.017 0.002 PHE B1872 TYR 0.021 0.001 TYR A 144 ARG 0.003 0.001 ARG A 306 *********************** 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 : 1.116 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: A 232 MET cc_start: 0.5254 (ptm) cc_final: 0.4695 (ptm) REVERT: A 407 PHE cc_start: 0.3839 (p90) cc_final: 0.3593 (p90) REVERT: B 1736 MET cc_start: 0.6433 (tpt) cc_final: 0.6158 (tpp) REVERT: B 1755 TYR cc_start: 0.7567 (p90) cc_final: 0.7337 (p90) REVERT: B 1801 HIS cc_start: 0.7575 (m-70) cc_final: 0.7226 (m-70) REVERT: B 1903 TYR cc_start: 0.6273 (t80) cc_final: 0.5725 (t80) REVERT: B 1905 GLU cc_start: 0.4699 (mt-10) cc_final: 0.4436 (mt-10) REVERT: B 2075 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5570 (pp) REVERT: B 2120 MET cc_start: 0.2084 (mmp) cc_final: 0.1849 (mmt) outliers start: 75 outliers final: 21 residues processed: 243 average time/residue: 0.2001 time to fit residues: 68.0714 Evaluate side-chains 156 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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: 9.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS B1547 ASN B1670 ASN B1713 HIS B1778 HIS ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6132 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9746 Z= 0.224 Angle : 0.765 9.012 13184 Z= 0.389 Chirality : 0.049 0.177 1403 Planarity : 0.006 0.065 1689 Dihedral : 7.264 29.781 1282 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.31 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -5.49 (0.20), residues: 1153 helix: -4.60 (0.59), residues: 25 sheet: -3.99 (0.31), residues: 209 loop : -3.89 (0.17), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B2094 HIS 0.007 0.001 HIS A 242 PHE 0.031 0.002 PHE A 574 TYR 0.022 0.002 TYR B2129 ARG 0.003 0.000 ARG A 475 *********************** 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 173 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6666 (m-10) cc_final: 0.5661 (m-80) REVERT: A 90 ARG cc_start: 0.5977 (ptt90) cc_final: 0.5747 (ptt180) REVERT: A 551 LYS cc_start: 0.6082 (mttt) cc_final: 0.5677 (mptt) REVERT: A 609 HIS cc_start: 0.6632 (m170) cc_final: 0.6158 (m-70) REVERT: B 1746 MET cc_start: 0.8027 (tpp) cc_final: 0.7780 (tpp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2394 time to fit residues: 57.1687 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 1.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 251 ASN A 541 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9746 Z= 0.355 Angle : 0.888 9.536 13184 Z= 0.455 Chirality : 0.052 0.230 1403 Planarity : 0.007 0.068 1689 Dihedral : 8.062 30.075 1282 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 37.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 25.07 % Favored : 74.76 % Rotamer: Outliers : 0.10 % Allowed : 8.42 % Favored : 91.48 % 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: -5.58 (0.20), residues: 1153 helix: -4.99 (0.41), residues: 33 sheet: -4.02 (0.30), residues: 224 loop : -3.92 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B2094 HIS 0.007 0.002 HIS A 597 PHE 0.016 0.002 PHE A 376 TYR 0.020 0.003 TYR A 44 ARG 0.006 0.001 ARG B1698 *********************** 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 142 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6739 (m-10) cc_final: 0.5617 (m-80) REVERT: A 232 MET cc_start: 0.6164 (ptm) cc_final: 0.5440 (ptm) REVERT: A 410 MET cc_start: 0.7336 (mmp) cc_final: 0.7082 (tpt) REVERT: A 475 ARG cc_start: 0.7674 (mtt90) cc_final: 0.6913 (ttp-110) REVERT: A 551 LYS cc_start: 0.6201 (mttt) cc_final: 0.5820 (mptt) REVERT: B 1734 MET cc_start: 0.6337 (mmt) cc_final: 0.5696 (mmm) REVERT: B 1809 GLN cc_start: 0.7536 (pm20) cc_final: 0.7148 (pm20) REVERT: B 1846 MET cc_start: 0.6589 (ttm) cc_final: 0.6263 (ttp) REVERT: B 2120 MET cc_start: 0.3752 (mmp) cc_final: 0.3517 (mmp) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.2019 time to fit residues: 40.8538 Evaluate side-chains 116 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 4.9990 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 0.0770 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- 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** B1553 ASN ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1973 GLN ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2076 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9746 Z= 0.324 Angle : 0.870 10.067 13184 Z= 0.442 Chirality : 0.052 0.214 1403 Planarity : 0.006 0.061 1689 Dihedral : 8.084 30.608 1282 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 21.16 % Favored : 78.75 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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: -5.55 (0.20), residues: 1153 helix: -4.93 (0.45), residues: 33 sheet: -4.10 (0.32), residues: 203 loop : -3.90 (0.17), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B2094 HIS 0.007 0.001 HIS B2159 PHE 0.050 0.003 PHE A 325 TYR 0.019 0.002 TYR A 44 ARG 0.005 0.001 ARG A 396 *********************** 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 147 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.151 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: A 63 TYR cc_start: 0.6719 (m-10) cc_final: 0.5611 (m-80) REVERT: A 232 MET cc_start: 0.6240 (ptm) cc_final: 0.5940 (ptm) REVERT: A 404 LYS cc_start: 0.8379 (mttp) cc_final: 0.8152 (mttm) REVERT: A 495 LEU cc_start: 0.8619 (tp) cc_final: 0.8417 (tp) REVERT: B 1703 TYR cc_start: 0.5083 (p90) cc_final: 0.4871 (p90) REVERT: B 1734 MET cc_start: 0.6389 (mmt) cc_final: 0.5784 (mmm) REVERT: B 1801 HIS cc_start: 0.7451 (m-70) cc_final: 0.6552 (m170) REVERT: B 1809 GLN cc_start: 0.7420 (pm20) cc_final: 0.7042 (pm20) REVERT: B 1829 HIS cc_start: 0.6431 (t-170) cc_final: 0.6228 (t70) REVERT: B 1850 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6651 (mmtt) REVERT: B 2120 MET cc_start: 0.3927 (mmt) cc_final: 0.3534 (mmp) REVERT: B 2180 TRP cc_start: 0.6797 (m100) cc_final: 0.6444 (m100) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2218 time to fit residues: 45.8238 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN B2076 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: 0.6308 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9746 Z= 0.243 Angle : 0.787 9.898 13184 Z= 0.400 Chirality : 0.049 0.226 1403 Planarity : 0.006 0.059 1689 Dihedral : 7.550 29.738 1282 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 20.90 % Favored : 79.01 % Rotamer: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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: -5.34 (0.21), residues: 1153 helix: -4.91 (0.42), residues: 33 sheet: -4.01 (0.34), residues: 190 loop : -3.74 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B2094 HIS 0.006 0.001 HIS B1801 PHE 0.023 0.002 PHE B1872 TYR 0.017 0.002 TYR A 144 ARG 0.003 0.000 ARG A 396 *********************** 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 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.146 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: A 63 TYR cc_start: 0.6835 (m-10) cc_final: 0.5915 (m-80) REVERT: A 232 MET cc_start: 0.6866 (ptm) cc_final: 0.6135 (ptm) REVERT: A 321 ARG cc_start: 0.6294 (ttt180) cc_final: 0.6042 (ttt180) REVERT: A 325 PHE cc_start: 0.6262 (m-80) cc_final: 0.6000 (m-10) REVERT: A 405 ILE cc_start: 0.7705 (mp) cc_final: 0.7479 (mm) REVERT: A 410 MET cc_start: 0.7468 (mmm) cc_final: 0.7248 (tpt) REVERT: B 1738 MET cc_start: 0.5812 (tpp) cc_final: 0.5350 (tpt) REVERT: B 1801 HIS cc_start: 0.7550 (m-70) cc_final: 0.6856 (m-70) REVERT: B 1809 GLN cc_start: 0.7370 (pm20) cc_final: 0.7082 (pm20) REVERT: B 1883 MET cc_start: 0.4804 (tmm) cc_final: 0.4273 (tmm) REVERT: B 2120 MET cc_start: 0.3363 (mmt) cc_final: 0.3063 (mmp) REVERT: B 2180 TRP cc_start: 0.6513 (m100) cc_final: 0.6114 (m100) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2188 time to fit residues: 47.4710 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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: 20.0000 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 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: 0.6234 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9746 Z= 0.216 Angle : 0.754 9.774 13184 Z= 0.382 Chirality : 0.049 0.251 1403 Planarity : 0.006 0.065 1689 Dihedral : 7.190 31.030 1282 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.47 % Favored : 81.44 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: -4.61 (0.51), residues: 27 sheet: -3.74 (0.34), residues: 198 loop : -3.64 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B2094 HIS 0.007 0.001 HIS B2159 PHE 0.021 0.002 PHE B1872 TYR 0.017 0.002 TYR A 418 ARG 0.005 0.000 ARG A 321 *********************** 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 157 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.057 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: A 63 TYR cc_start: 0.6805 (m-10) cc_final: 0.5871 (m-80) REVERT: A 232 MET cc_start: 0.7005 (ptm) cc_final: 0.6146 (ptm) REVERT: A 233 SER cc_start: 0.8540 (p) cc_final: 0.8333 (m) REVERT: A 405 ILE cc_start: 0.7718 (mp) cc_final: 0.7482 (mm) REVERT: A 410 MET cc_start: 0.7420 (mmm) cc_final: 0.7204 (tpt) REVERT: A 475 ARG cc_start: 0.7020 (ttm110) cc_final: 0.6667 (ttm170) REVERT: B 1801 HIS cc_start: 0.7555 (m-70) cc_final: 0.6817 (m-70) REVERT: B 1809 GLN cc_start: 0.7381 (pm20) cc_final: 0.7093 (pm20) REVERT: B 1883 MET cc_start: 0.4871 (tmm) cc_final: 0.4522 (tmm) REVERT: B 1988 MET cc_start: 0.1964 (mtp) cc_final: 0.1756 (mtp) REVERT: B 2120 MET cc_start: 0.3355 (mmt) cc_final: 0.3102 (mmp) REVERT: B 2180 TRP cc_start: 0.6318 (m100) cc_final: 0.5940 (m100) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2138 time to fit residues: 47.0974 Evaluate side-chains 125 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9746 Z= 0.225 Angle : 0.752 9.578 13184 Z= 0.379 Chirality : 0.049 0.252 1403 Planarity : 0.006 0.070 1689 Dihedral : 7.111 32.633 1282 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 19.69 % Favored : 80.23 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: -5.07 (0.21), residues: 1153 helix: -4.40 (0.60), residues: 27 sheet: -3.73 (0.34), residues: 198 loop : -3.59 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B2094 HIS 0.020 0.002 HIS A 252 PHE 0.028 0.002 PHE B1816 TYR 0.016 0.002 TYR A 144 ARG 0.005 0.000 ARG A 321 *********************** 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 149 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.113 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: A 229 LEU cc_start: 0.6140 (mp) cc_final: 0.5781 (mp) REVERT: A 232 MET cc_start: 0.7141 (ptm) cc_final: 0.6232 (ptm) REVERT: A 405 ILE cc_start: 0.7789 (mp) cc_final: 0.7552 (mm) REVERT: A 410 MET cc_start: 0.7398 (mmm) cc_final: 0.7173 (tpt) REVERT: A 475 ARG cc_start: 0.7022 (ttm110) cc_final: 0.6699 (ttm170) REVERT: A 483 ILE cc_start: 0.7087 (mt) cc_final: 0.6881 (mt) REVERT: B 1700 TRP cc_start: 0.7528 (m100) cc_final: 0.7199 (m100) REVERT: B 1801 HIS cc_start: 0.7558 (m-70) cc_final: 0.6973 (m-70) REVERT: B 1809 GLN cc_start: 0.7327 (pm20) cc_final: 0.7110 (pm20) REVERT: B 1883 MET cc_start: 0.4758 (tmm) cc_final: 0.4524 (tmm) REVERT: B 1988 MET cc_start: 0.1892 (mtp) cc_final: 0.1686 (mtp) REVERT: B 2120 MET cc_start: 0.3378 (mmt) cc_final: 0.3124 (mmp) REVERT: B 2180 TRP cc_start: 0.6291 (m100) cc_final: 0.5993 (m100) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2037 time to fit residues: 43.4609 Evaluate side-chains 122 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9746 Z= 0.226 Angle : 0.757 9.686 13184 Z= 0.383 Chirality : 0.049 0.305 1403 Planarity : 0.006 0.060 1689 Dihedral : 7.083 31.910 1282 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.65 % Favored : 81.27 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -5.04 (0.22), residues: 1153 helix: -4.58 (0.48), residues: 33 sheet: -3.70 (0.35), residues: 188 loop : -3.56 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B2094 HIS 0.023 0.002 HIS A 252 PHE 0.019 0.002 PHE B1872 TYR 0.015 0.002 TYR A 418 ARG 0.004 0.000 ARG A 321 *********************** 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 144 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.100 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: A 63 TYR cc_start: 0.6659 (m-10) cc_final: 0.5833 (m-80) REVERT: A 229 LEU cc_start: 0.6258 (mp) cc_final: 0.5866 (mp) REVERT: A 232 MET cc_start: 0.6858 (ptm) cc_final: 0.6276 (ptm) REVERT: A 404 LYS cc_start: 0.8424 (mttp) cc_final: 0.8212 (mttm) REVERT: A 405 ILE cc_start: 0.7607 (mp) cc_final: 0.7391 (mm) REVERT: A 410 MET cc_start: 0.7402 (mmm) cc_final: 0.7169 (tpt) REVERT: A 475 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6834 (ttm170) REVERT: A 483 ILE cc_start: 0.6879 (mt) cc_final: 0.6412 (mt) REVERT: B 1801 HIS cc_start: 0.7476 (m-70) cc_final: 0.6975 (m-70) REVERT: B 1874 ILE cc_start: 0.6748 (mp) cc_final: 0.6425 (mp) REVERT: B 2120 MET cc_start: 0.3305 (mmt) cc_final: 0.3058 (mmp) REVERT: B 2180 TRP cc_start: 0.6328 (m100) cc_final: 0.6024 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2248 time to fit residues: 46.2098 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 10.0000 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 82 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 251 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1729 HIS ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1809 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.3739 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= 0.188 Angle : 0.719 8.658 13184 Z= 0.362 Chirality : 0.048 0.271 1403 Planarity : 0.005 0.056 1689 Dihedral : 6.662 30.035 1282 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.87 % Favored : 84.04 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -4.83 (0.22), residues: 1153 helix: -4.53 (0.51), residues: 32 sheet: -3.57 (0.38), residues: 168 loop : -3.43 (0.18), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B2094 HIS 0.007 0.001 HIS B1801 PHE 0.017 0.001 PHE B1872 TYR 0.018 0.001 TYR B2129 ARG 0.006 0.000 ARG A 90 *********************** 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 161 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6612 (m-10) cc_final: 0.5830 (m-80) REVERT: A 93 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7683 (mmtt) REVERT: A 229 LEU cc_start: 0.6020 (mp) cc_final: 0.5687 (mp) REVERT: B 1547 ASN cc_start: 0.7794 (t0) cc_final: 0.7575 (t0) REVERT: B 1801 HIS cc_start: 0.7293 (m-70) cc_final: 0.6763 (m-70) REVERT: B 1874 ILE cc_start: 0.6497 (mp) cc_final: 0.6153 (mp) REVERT: B 1883 MET cc_start: 0.4035 (tmm) cc_final: 0.3353 (tmm) REVERT: B 2120 MET cc_start: 0.3381 (mmt) cc_final: 0.3134 (mmp) REVERT: B 2180 TRP cc_start: 0.6306 (m100) cc_final: 0.5871 (m100) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1960 time to fit residues: 45.3632 Evaluate side-chains 126 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 246 GLN A 251 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9746 Z= 0.225 Angle : 0.759 10.658 13184 Z= 0.385 Chirality : 0.049 0.265 1403 Planarity : 0.006 0.093 1689 Dihedral : 6.881 33.538 1282 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.52 % Favored : 82.39 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -4.78 (0.22), residues: 1153 helix: -4.36 (0.55), residues: 33 sheet: -3.51 (0.40), residues: 160 loop : -3.41 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 322 HIS 0.006 0.001 HIS B1801 PHE 0.023 0.002 PHE A 179 TYR 0.023 0.002 TYR B2129 ARG 0.006 0.000 ARG A 90 ********************** 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 144 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.183 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: A 63 TYR cc_start: 0.6674 (m-10) cc_final: 0.5889 (m-80) REVERT: A 93 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7760 (mmtt) REVERT: A 229 LEU cc_start: 0.6025 (mp) cc_final: 0.5754 (mp) REVERT: B 1874 ILE cc_start: 0.6422 (mp) cc_final: 0.6119 (mp) REVERT: B 1883 MET cc_start: 0.4405 (tmm) cc_final: 0.3663 (tmm) REVERT: B 2180 TRP cc_start: 0.6801 (m100) cc_final: 0.6391 (m100) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1952 time to fit residues: 40.6697 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 0.0030 chunk 85 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 81 optimal weight: 2.9990 overall best weight: 1.8112 ------------------------------------------------------------------------------- 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.151952 restraints weight = 27860.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153658 restraints weight = 18879.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.154957 restraints weight = 13768.463| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.3980 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= 0.217 Angle : 0.737 8.635 13184 Z= 0.373 Chirality : 0.048 0.251 1403 Planarity : 0.006 0.089 1689 Dihedral : 6.824 30.877 1282 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.35 % Favored : 82.57 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -4.74 (0.22), residues: 1153 helix: -4.37 (0.54), residues: 33 sheet: -3.38 (0.40), residues: 170 loop : -3.38 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B2094 HIS 0.005 0.001 HIS B1778 PHE 0.017 0.002 PHE B1872 TYR 0.021 0.002 TYR B2129 ARG 0.006 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.19 seconds wall clock time: 35 minutes 43.49 seconds (2143.49 seconds total)