Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 19:28:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/10_2023/7kxy_23067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/10_2023/7kxy_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_23067/10_2023/7kxy_23067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/10_2023/7kxy_23067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/10_2023/7kxy_23067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/10_2023/7kxy_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-1.21rc1-5097/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: 5.43, per 1000 atoms: 0.57 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: 3.51 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: 0.66 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: 2.12 Time building geometry restraints manager: 3.82 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: 1.100 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: 3.890 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 26.870 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.135 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: 0.2233 time to fit residues: 76.3354 Evaluate side-chains 155 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1224 time to fit residues: 5.8913 ------------------------------------------------------------------------------- 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** B1819 GLN ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.2405 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= 0.191 Angle : 0.741 8.729 13184 Z= 0.375 Chirality : 0.049 0.196 1403 Planarity : 0.005 0.060 1689 Dihedral : 7.025 30.423 1282 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.26 % Favored : 84.65 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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: -5.41 (0.20), residues: 1153 helix: -4.57 (0.60), residues: 24 sheet: -3.94 (0.32), residues: 206 loop : -3.84 (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 : 1.117 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 outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2397 time to fit residues: 58.1646 Evaluate side-chains 127 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5367 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 251 ASN A 541 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1713 HIS ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2132 GLN ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9746 Z= 0.276 Angle : 0.796 9.082 13184 Z= 0.406 Chirality : 0.050 0.225 1403 Planarity : 0.006 0.059 1689 Dihedral : 7.369 28.543 1282 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 30.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 22.20 % Favored : 77.71 % Rotamer: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % 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: -5.37 (0.21), residues: 1153 helix: -4.94 (0.43), residues: 32 sheet: -3.94 (0.31), residues: 225 loop : -3.73 (0.18), residues: 896 *********************** 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 147 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.129 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 outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2369 time to fit residues: 48.3774 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5865 ------------------------------------------------------------------------------- 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: 8.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B1809 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** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9746 Z= 0.246 Angle : 0.779 9.307 13184 Z= 0.393 Chirality : 0.049 0.205 1403 Planarity : 0.006 0.080 1689 Dihedral : 7.327 33.086 1282 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.73 % Favored : 81.18 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: -5.23 (0.21), residues: 1153 helix: -4.86 (0.47), residues: 32 sheet: -3.89 (0.32), residues: 220 loop : -3.63 (0.18), residues: 901 *********************** 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 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.142 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 outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2261 time to fit residues: 48.2635 Evaluate side-chains 121 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5584 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** 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** 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: 0.6238 moved from start: 0.3176 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= 0.234 Angle : 0.778 10.105 13184 Z= 0.390 Chirality : 0.049 0.218 1403 Planarity : 0.006 0.058 1689 Dihedral : 7.165 33.736 1282 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 19.95 % Favored : 79.97 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: -5.15 (0.21), residues: 1153 helix: -4.79 (0.48), residues: 32 sheet: -4.00 (0.33), residues: 199 loop : -3.56 (0.18), residues: 922 *********************** 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 : 1.093 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: 151 average time/residue: 0.2387 time to fit residues: 50.0802 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6188 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 chunk 59 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- 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 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** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9746 Z= 0.285 Angle : 0.816 10.240 13184 Z= 0.414 Chirality : 0.050 0.258 1403 Planarity : 0.006 0.057 1689 Dihedral : 7.573 33.200 1282 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 32.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 21.42 % Favored : 78.49 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: -5.25 (0.21), residues: 1153 helix: -4.70 (0.51), residues: 32 sheet: -4.01 (0.33), residues: 189 loop : -3.67 (0.17), residues: 932 *********************** 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 146 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.075 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: 146 average time/residue: 0.2075 time to fit residues: 43.7576 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4455 ------------------------------------------------------------------------------- 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: 8.9990 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 149 ASN ** 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 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1547 ASN B1864 GLN 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: 0.6272 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9746 Z= 0.256 Angle : 0.805 10.363 13184 Z= 0.403 Chirality : 0.049 0.254 1403 Planarity : 0.006 0.066 1689 Dihedral : 7.387 33.223 1282 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 19.95 % Favored : 79.97 % Rotamer: Outliers : 0.10 % Allowed : 2.49 % Favored : 97.42 % 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: -5.21 (0.21), residues: 1153 helix: -4.65 (0.53), residues: 32 sheet: -4.05 (0.32), residues: 198 loop : -3.61 (0.18), residues: 923 *********************** 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 148 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.062 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 outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.2224 time to fit residues: 47.1716 Evaluate side-chains 117 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5047 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9746 Z= 0.179 Angle : 0.739 9.224 13184 Z= 0.366 Chirality : 0.048 0.281 1403 Planarity : 0.005 0.059 1689 Dihedral : 6.714 35.974 1282 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.74 % Favored : 85.17 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -4.85 (0.22), residues: 1153 helix: -4.76 (0.48), residues: 30 sheet: -3.56 (0.34), residues: 208 loop : -3.39 (0.18), residues: 915 *********************** 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 152 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.154 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: 152 average time/residue: 0.2130 time to fit residues: 46.5908 Evaluate side-chains 122 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4213 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9746 Z= 0.187 Angle : 0.731 10.635 13184 Z= 0.361 Chirality : 0.048 0.260 1403 Planarity : 0.006 0.089 1689 Dihedral : 6.566 32.473 1282 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.13 % Favored : 83.78 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -4.71 (0.22), residues: 1153 helix: -4.23 (0.68), residues: 25 sheet: -3.51 (0.37), residues: 180 loop : -3.34 (0.18), residues: 948 *********************** 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 144 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.115 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: 144 average time/residue: 0.2168 time to fit residues: 44.5902 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6421 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1729 HIS B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.4056 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= 0.180 Angle : 0.727 9.439 13184 Z= 0.359 Chirality : 0.048 0.241 1403 Planarity : 0.006 0.083 1689 Dihedral : 6.376 29.648 1282 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.79 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -4.65 (0.22), residues: 1153 helix: -4.40 (0.55), residues: 31 sheet: -3.45 (0.36), residues: 185 loop : -3.27 (0.18), residues: 937 ********************** 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 151 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.120 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: 151 average time/residue: 0.2008 time to fit residues: 44.3861 Evaluate side-chains 122 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6306 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 0.0670 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 95 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 0.9478 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1778 HIS B1829 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.168675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.157610 restraints weight = 27557.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.159632 restraints weight = 18361.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.161082 restraints weight = 13181.986| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.4259 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= 0.182 Angle : 0.718 9.172 13184 Z= 0.355 Chirality : 0.047 0.241 1403 Planarity : 0.006 0.079 1689 Dihedral : 6.311 29.899 1282 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.00 % Favored : 84.91 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.33 % 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: -4.55 (0.22), residues: 1153 helix: -4.29 (0.62), residues: 24 sheet: -3.46 (0.37), residues: 180 loop : -3.20 (0.18), residues: 949 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.33 seconds wall clock time: 38 minutes 18.38 seconds (2298.38 seconds total)