Starting phenix.real_space_refine on Tue Mar 3 14:16:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey0_31374/03_2026/7ey0_31374.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 24 5.16 5 C 3824 2.51 5 N 994 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5963 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "B" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 564 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 7, 'TRANS': 65} Chain breaks: 4 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Time building chain proxies: 1.33, per 1000 atoms: 0.22 Number of scatterers: 5963 At special positions: 0 Unit cell: (79.92, 117.72, 123.12, 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 24 16.00 O 1121 8.00 N 994 7.00 C 3824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 86 " distance=2.07 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.47 Conformation dependent library (CDL) restraints added in 350.9 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 17 sheets defined 8.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.623A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.526A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.561A pdb=" N THR H 90 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.511A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.452A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.584A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.473A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 7 current: chain 'A' and resid 78 through 83 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 50 removed outlier: 6.678A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 97 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 104 through 108 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.526A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR L 69 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'L' and resid 91 through 92 removed outlier: 3.874A pdb=" N LEU L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.256A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.595A pdb=" N SER B 61 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.577A pdb=" N VAL B 88 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 97 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 90 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 3.767A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 255 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: 0.85 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 949 1.31 - 1.45: 2124 1.45 - 1.59: 3010 1.59 - 1.74: 0 1.74 - 1.88: 31 Bond restraints: 6114 Sorted by residual: bond pdb=" C PRO B 96 " pdb=" O PRO B 96 " ideal model delta sigma weight residual 1.233 1.172 0.060 1.16e-02 7.43e+03 2.71e+01 bond pdb=" C PRO B 6 " pdb=" O PRO B 6 " ideal model delta sigma weight residual 1.246 1.204 0.041 8.50e-03 1.38e+04 2.37e+01 bond pdb=" C PRO B 42 " pdb=" O PRO B 42 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.53e+01 bond pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.34e-02 5.57e+03 9.76e+00 ... (remaining 6109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 8131 3.09 - 6.19: 144 6.19 - 9.28: 10 9.28 - 12.37: 5 12.37 - 15.46: 3 Bond angle restraints: 8293 Sorted by residual: angle pdb=" C PRO B 96 " pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 111.46 100.25 11.21 1.29e+00 6.01e-01 7.55e+01 angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 110.29 97.27 13.02 1.64e+00 3.72e-01 6.30e+01 angle pdb=" C GLN B 87 " pdb=" CA GLN B 87 " pdb=" CB GLN B 87 " ideal model delta sigma weight residual 111.74 99.57 12.17 1.59e+00 3.96e-01 5.86e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 129.86 -15.46 2.30e+00 1.89e-01 4.52e+01 angle pdb=" C GLN B 95 " pdb=" CA GLN B 95 " pdb=" CB GLN B 95 " ideal model delta sigma weight residual 109.45 99.97 9.48 1.45e+00 4.76e-01 4.27e+01 ... (remaining 8288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3172 17.35 - 34.70: 290 34.70 - 52.05: 59 52.05 - 69.41: 15 69.41 - 86.76: 10 Dihedral angle restraints: 3546 sinusoidal: 1375 harmonic: 2171 Sorted by residual: dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -13.29 -72.71 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" CA THR H 101 " pdb=" C THR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 3543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 788 0.092 - 0.183: 84 0.183 - 0.275: 14 0.275 - 0.367: 4 0.367 - 0.458: 2 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA PHE B 98 " pdb=" N PHE B 98 " pdb=" C PHE B 98 " pdb=" CB PHE B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA GLN B 5 " pdb=" N GLN B 5 " pdb=" C GLN B 5 " pdb=" CB GLN B 5 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA GLN B 95 " pdb=" N GLN B 95 " pdb=" C GLN B 95 " pdb=" CB GLN B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 889 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO L 80 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 97 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL B 97 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 97 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE B 98 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " -0.015 2.00e-02 2.50e+03 2.09e-02 8.71e+00 pdb=" CG TYR H 33 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 185 2.66 - 3.22: 5667 3.22 - 3.78: 8987 3.78 - 4.34: 12996 4.34 - 4.90: 21645 Nonbonded interactions: 49480 Sorted by model distance: nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLY H 111 " model vdw 2.105 3.120 nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.149 3.040 nonbonded pdb=" OG SER R 469 " pdb=" OE1 GLU R 471 " model vdw 2.170 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.196 3.040 nonbonded pdb=" NE2 GLN B 5 " pdb=" SG CYS B 21 " model vdw 2.199 3.480 ... (remaining 49475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.400 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.007 0.068 6122 Z= 0.391 Angle : 1.026 15.464 8309 Z= 0.621 Chirality : 0.064 0.458 892 Planarity : 0.007 0.097 1058 Dihedral : 14.511 86.758 2138 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.24 % Favored : 87.34 % Rotamer: Outliers : 3.08 % Allowed : 0.62 % Favored : 96.31 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.31), residues: 719 helix: -2.18 (1.14), residues: 21 sheet: -1.17 (0.36), residues: 217 loop : -1.88 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 44 TYR 0.048 0.002 TYR H 33 PHE 0.030 0.002 PHE B 98 TRP 0.017 0.003 TRP H 47 HIS 0.012 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00717 ( 6114) covalent geometry : angle 1.00684 ( 8293) SS BOND : bond 0.01457 ( 8) SS BOND : angle 4.62628 ( 16) hydrogen bonds : bond 0.25239 ( 111) hydrogen bonds : angle 11.12190 ( 255) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 471 GLU cc_start: 0.7604 (mp0) cc_final: 0.7355 (mp0) REVERT: B 38 PRO cc_start: 0.8488 (OUTLIER) cc_final: 0.8284 (Cg_endo) REVERT: B 40 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: B 47 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.4258 (p90) REVERT: B 87 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8491 (tm-30) REVERT: B 88 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 95 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: N 43 PHE cc_start: 0.5948 (p90) cc_final: 0.5165 (p90) REVERT: N 84 LEU cc_start: 0.7640 (mt) cc_final: 0.7405 (mp) REVERT: N 111 ASP cc_start: 0.8045 (t70) cc_final: 0.7560 (p0) REVERT: N 129 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7553 (ttpp) REVERT: N 132 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7794 (mt-10) REVERT: N 133 PHE cc_start: 0.7780 (m-80) cc_final: 0.7492 (m-10) REVERT: N 171 VAL cc_start: 0.8677 (t) cc_final: 0.8441 (p) REVERT: N 202 LYS cc_start: 0.8234 (mttt) cc_final: 0.7935 (mttp) REVERT: N 231 ILE cc_start: 0.8945 (mm) cc_final: 0.8556 (pt) REVERT: N 237 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7905 (ptp90) outliers start: 20 outliers final: 3 residues processed: 206 average time/residue: 0.0942 time to fit residues: 24.0818 Evaluate side-chains 171 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 PRO Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 42 PRO Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124938 restraints weight = 9587.694| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.36 r_work: 0.3390 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6122 Z= 0.181 Angle : 0.697 10.996 8309 Z= 0.366 Chirality : 0.047 0.174 892 Planarity : 0.005 0.069 1058 Dihedral : 8.660 88.813 845 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.08 % Allowed : 10.77 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.32), residues: 719 helix: -2.04 (1.16), residues: 21 sheet: -0.90 (0.36), residues: 218 loop : -1.63 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 273 TYR 0.021 0.001 TYR H 33 PHE 0.015 0.002 PHE R 456 TRP 0.015 0.002 TRP N 64 HIS 0.006 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6114) covalent geometry : angle 0.68021 ( 8293) SS BOND : bond 0.00611 ( 8) SS BOND : angle 3.49015 ( 16) hydrogen bonds : bond 0.03697 ( 111) hydrogen bonds : angle 7.93171 ( 255) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 5 GLN cc_start: 0.6855 (tp40) cc_final: 0.6643 (tp40) REVERT: B 47 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.4859 (p90) REVERT: B 87 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: B 95 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: B 103 LYS cc_start: 0.8657 (tttt) cc_final: 0.8248 (tptp) REVERT: N 43 PHE cc_start: 0.6788 (p90) cc_final: 0.5432 (p90) REVERT: N 62 VAL cc_start: 0.8597 (t) cc_final: 0.8058 (p) REVERT: N 111 ASP cc_start: 0.8455 (t70) cc_final: 0.7597 (p0) REVERT: N 112 SER cc_start: 0.9069 (p) cc_final: 0.8092 (t) REVERT: N 129 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8041 (mtpp) REVERT: N 190 ARG cc_start: 0.7318 (mtp-110) cc_final: 0.6749 (mpt180) outliers start: 20 outliers final: 11 residues processed: 198 average time/residue: 0.0842 time to fit residues: 21.1648 Evaluate side-chains 172 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119298 restraints weight = 9538.077| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.02 r_work: 0.3417 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6122 Z= 0.169 Angle : 0.657 9.841 8309 Z= 0.345 Chirality : 0.046 0.163 892 Planarity : 0.004 0.058 1058 Dihedral : 7.099 89.463 830 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.31 % Allowed : 14.15 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.31), residues: 719 helix: -2.27 (1.04), residues: 21 sheet: -0.81 (0.36), residues: 226 loop : -1.51 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 273 TYR 0.014 0.001 TYR L 49 PHE 0.029 0.002 PHE N 32 TRP 0.014 0.001 TRP N 64 HIS 0.005 0.001 HIS N 49 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6114) covalent geometry : angle 0.64065 ( 8293) SS BOND : bond 0.00645 ( 8) SS BOND : angle 3.36933 ( 16) hydrogen bonds : bond 0.03484 ( 111) hydrogen bonds : angle 7.31720 ( 255) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8256 (tm-30) REVERT: L 82 ASP cc_start: 0.8544 (m-30) cc_final: 0.8303 (m-30) REVERT: R 434 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8215 (pt) REVERT: R 442 ASP cc_start: 0.8242 (m-30) cc_final: 0.7987 (m-30) REVERT: B 47 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.4480 (p90) REVERT: B 87 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: B 94 ASP cc_start: 0.8090 (t70) cc_final: 0.7758 (t70) REVERT: B 103 LYS cc_start: 0.8603 (tttt) cc_final: 0.8241 (tptp) REVERT: N 43 PHE cc_start: 0.6787 (p90) cc_final: 0.5509 (p90) REVERT: N 111 ASP cc_start: 0.8372 (t70) cc_final: 0.7716 (p0) REVERT: N 112 SER cc_start: 0.8786 (p) cc_final: 0.8168 (t) REVERT: N 129 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7996 (mtpp) REVERT: N 190 ARG cc_start: 0.7176 (mtp-110) cc_final: 0.6757 (mpt180) outliers start: 28 outliers final: 17 residues processed: 189 average time/residue: 0.0857 time to fit residues: 20.3495 Evaluate side-chains 186 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119653 restraints weight = 9583.246| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.83 r_work: 0.3401 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6122 Z= 0.168 Angle : 0.633 9.891 8309 Z= 0.333 Chirality : 0.045 0.152 892 Planarity : 0.004 0.055 1058 Dihedral : 6.562 89.861 827 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.54 % Allowed : 14.77 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.31), residues: 719 helix: -2.58 (0.95), residues: 21 sheet: -0.76 (0.35), residues: 228 loop : -1.48 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 49 PHE 0.024 0.001 PHE N 32 TRP 0.014 0.001 TRP N 64 HIS 0.004 0.001 HIS N 49 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6114) covalent geometry : angle 0.61719 ( 8293) SS BOND : bond 0.00522 ( 8) SS BOND : angle 3.29961 ( 16) hydrogen bonds : bond 0.03261 ( 111) hydrogen bonds : angle 6.83798 ( 255) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8277 (tm-30) REVERT: R 434 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8142 (pt) REVERT: R 442 ASP cc_start: 0.8269 (m-30) cc_final: 0.7967 (m-30) REVERT: R 471 GLU cc_start: 0.8182 (mp0) cc_final: 0.7981 (mp0) REVERT: B 46 MET cc_start: 0.5652 (ttp) cc_final: 0.5346 (ttt) REVERT: B 47 TYR cc_start: 0.4726 (OUTLIER) cc_final: 0.4234 (p90) REVERT: B 94 ASP cc_start: 0.8101 (t70) cc_final: 0.7798 (t70) REVERT: B 103 LYS cc_start: 0.8583 (tttt) cc_final: 0.8245 (tptp) REVERT: N 32 PHE cc_start: 0.5229 (p90) cc_final: 0.4971 (p90) REVERT: N 43 PHE cc_start: 0.6795 (p90) cc_final: 0.5515 (p90) REVERT: N 111 ASP cc_start: 0.8387 (t70) cc_final: 0.8166 (p0) REVERT: N 129 LYS cc_start: 0.8296 (mtmt) cc_final: 0.8095 (mtpp) REVERT: N 190 ARG cc_start: 0.7310 (mtp-110) cc_final: 0.7025 (mmp-170) outliers start: 36 outliers final: 28 residues processed: 193 average time/residue: 0.0875 time to fit residues: 21.4269 Evaluate side-chains 191 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain R residue 378 LYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 0.0770 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 32 HIS ** 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 = 0.3972 r_free = 0.3972 target = 0.150319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116311 restraints weight = 9720.453| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.84 r_work: 0.3395 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6122 Z= 0.145 Angle : 0.615 8.951 8309 Z= 0.322 Chirality : 0.045 0.145 892 Planarity : 0.004 0.051 1058 Dihedral : 6.286 84.648 827 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.54 % Allowed : 16.77 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.31), residues: 719 helix: -2.82 (0.87), residues: 21 sheet: -0.62 (0.35), residues: 228 loop : -1.42 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.014 0.001 TYR L 49 PHE 0.022 0.001 PHE H 67 TRP 0.011 0.001 TRP N 64 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6114) covalent geometry : angle 0.60063 ( 8293) SS BOND : bond 0.00456 ( 8) SS BOND : angle 3.04912 ( 16) hydrogen bonds : bond 0.03035 ( 111) hydrogen bonds : angle 6.63029 ( 255) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.7984 (tp30) cc_final: 0.7754 (tp30) REVERT: H 67 PHE cc_start: 0.8371 (m-10) cc_final: 0.8107 (m-80) REVERT: L 38 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8377 (tm-30) REVERT: R 442 ASP cc_start: 0.8275 (m-30) cc_final: 0.7959 (m-30) REVERT: R 471 GLU cc_start: 0.8100 (mp0) cc_final: 0.7884 (mp0) REVERT: B 5 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6427 (mm110) REVERT: B 46 MET cc_start: 0.5715 (ttp) cc_final: 0.5497 (ttp) REVERT: B 47 TYR cc_start: 0.4988 (OUTLIER) cc_final: 0.4307 (p90) REVERT: B 72 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7303 (mp) REVERT: B 94 ASP cc_start: 0.8114 (t70) cc_final: 0.7828 (t70) REVERT: B 103 LYS cc_start: 0.8567 (tttt) cc_final: 0.8258 (tptt) REVERT: N 43 PHE cc_start: 0.6714 (p90) cc_final: 0.5400 (p90) REVERT: N 129 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7980 (mtpp) REVERT: N 190 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6970 (mmp-170) outliers start: 36 outliers final: 26 residues processed: 191 average time/residue: 0.0809 time to fit residues: 19.7216 Evaluate side-chains 195 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118216 restraints weight = 9617.492| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.00 r_work: 0.3404 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6122 Z= 0.163 Angle : 0.631 9.035 8309 Z= 0.329 Chirality : 0.045 0.151 892 Planarity : 0.004 0.050 1058 Dihedral : 5.442 49.127 824 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.08 % Allowed : 18.77 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 719 helix: -3.18 (0.73), residues: 27 sheet: -0.64 (0.35), residues: 230 loop : -1.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.015 0.001 TYR H 107 PHE 0.019 0.001 PHE R 342 TRP 0.012 0.001 TRP N 64 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6114) covalent geometry : angle 0.61798 ( 8293) SS BOND : bond 0.00465 ( 8) SS BOND : angle 3.02144 ( 16) hydrogen bonds : bond 0.03019 ( 111) hydrogen bonds : angle 6.48267 ( 255) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.7995 (tp30) cc_final: 0.7738 (tp30) REVERT: H 67 PHE cc_start: 0.8285 (m-10) cc_final: 0.7992 (m-80) REVERT: L 38 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8370 (tm-30) REVERT: R 442 ASP cc_start: 0.8287 (m-30) cc_final: 0.7992 (m-30) REVERT: R 471 GLU cc_start: 0.8120 (mp0) cc_final: 0.7915 (mp0) REVERT: B 5 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6574 (mm110) REVERT: B 46 MET cc_start: 0.5784 (ttp) cc_final: 0.5543 (ttp) REVERT: B 47 TYR cc_start: 0.4954 (OUTLIER) cc_final: 0.4265 (p90) REVERT: B 72 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7286 (mp) REVERT: B 94 ASP cc_start: 0.8171 (t70) cc_final: 0.7853 (t70) REVERT: N 43 PHE cc_start: 0.6812 (p90) cc_final: 0.5417 (p90) REVERT: N 115 GLN cc_start: 0.8612 (mm110) cc_final: 0.8311 (mm-40) REVERT: N 129 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7971 (mtpp) REVERT: N 190 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.7009 (mmp-170) outliers start: 33 outliers final: 27 residues processed: 190 average time/residue: 0.0800 time to fit residues: 19.2792 Evaluate side-chains 194 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 45 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 32 HIS N 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117236 restraints weight = 9661.027| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.78 r_work: 0.3409 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6122 Z= 0.137 Angle : 0.616 8.676 8309 Z= 0.322 Chirality : 0.044 0.184 892 Planarity : 0.004 0.048 1058 Dihedral : 5.385 47.350 824 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.62 % Allowed : 19.54 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.32), residues: 719 helix: -3.04 (0.78), residues: 27 sheet: -0.58 (0.36), residues: 230 loop : -1.27 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 49 PHE 0.022 0.001 PHE N 168 TRP 0.006 0.001 TRP R 436 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6114) covalent geometry : angle 0.59862 ( 8293) SS BOND : bond 0.00664 ( 8) SS BOND : angle 3.38346 ( 16) hydrogen bonds : bond 0.02768 ( 111) hydrogen bonds : angle 6.25474 ( 255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8012 (tp30) cc_final: 0.7472 (tp30) REVERT: H 67 PHE cc_start: 0.8016 (m-10) cc_final: 0.7634 (m-80) REVERT: L 38 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8368 (tm-30) REVERT: R 442 ASP cc_start: 0.8293 (m-30) cc_final: 0.8006 (m-30) REVERT: R 471 GLU cc_start: 0.8107 (mp0) cc_final: 0.7891 (mp0) REVERT: B 5 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6412 (mm110) REVERT: B 46 MET cc_start: 0.5827 (ttp) cc_final: 0.5569 (ttp) REVERT: B 47 TYR cc_start: 0.4925 (OUTLIER) cc_final: 0.4204 (p90) REVERT: B 72 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 94 ASP cc_start: 0.8238 (t70) cc_final: 0.7947 (t70) REVERT: N 43 PHE cc_start: 0.6782 (p90) cc_final: 0.5391 (p90) REVERT: N 111 ASP cc_start: 0.7646 (p0) cc_final: 0.7024 (p0) REVERT: N 115 GLN cc_start: 0.8581 (mm110) cc_final: 0.8280 (mm-40) REVERT: N 129 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7883 (ttpp) REVERT: N 190 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.7014 (mmp-170) outliers start: 30 outliers final: 22 residues processed: 193 average time/residue: 0.0864 time to fit residues: 21.1086 Evaluate side-chains 191 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 354 ASN B 5 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119920 restraints weight = 9622.274| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.98 r_work: 0.3384 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6122 Z= 0.201 Angle : 0.671 12.478 8309 Z= 0.350 Chirality : 0.046 0.181 892 Planarity : 0.004 0.047 1058 Dihedral : 5.434 47.018 824 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.23 % Allowed : 20.46 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.32), residues: 719 helix: -3.06 (0.78), residues: 27 sheet: -0.58 (0.35), residues: 229 loop : -1.33 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 273 TYR 0.017 0.002 TYR N 170 PHE 0.012 0.001 PHE H 67 TRP 0.006 0.001 TRP N 64 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 6114) covalent geometry : angle 0.65644 ( 8293) SS BOND : bond 0.00558 ( 8) SS BOND : angle 3.21412 ( 16) hydrogen bonds : bond 0.03055 ( 111) hydrogen bonds : angle 6.22188 ( 255) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8026 (tp30) cc_final: 0.7536 (tp30) REVERT: H 67 PHE cc_start: 0.8176 (m-10) cc_final: 0.7924 (m-80) REVERT: L 38 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8427 (tm-30) REVERT: R 442 ASP cc_start: 0.8248 (m-30) cc_final: 0.7954 (m-30) REVERT: B 47 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4524 (p90) REVERT: B 72 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7285 (mp) REVERT: B 94 ASP cc_start: 0.8057 (t70) cc_final: 0.7788 (t70) REVERT: B 103 LYS cc_start: 0.8359 (tptt) cc_final: 0.8061 (tptm) REVERT: N 43 PHE cc_start: 0.6835 (p90) cc_final: 0.5434 (p90) REVERT: N 115 GLN cc_start: 0.8584 (mm110) cc_final: 0.8357 (mm-40) REVERT: N 190 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7091 (mmp-170) outliers start: 34 outliers final: 29 residues processed: 185 average time/residue: 0.0860 time to fit residues: 20.0008 Evaluate side-chains 193 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** N 49 HIS ** 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 = 0.3987 r_free = 0.3987 target = 0.151085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.124343 restraints weight = 9588.620| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.38 r_work: 0.3379 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6122 Z= 0.152 Angle : 0.662 12.225 8309 Z= 0.345 Chirality : 0.045 0.156 892 Planarity : 0.004 0.046 1058 Dihedral : 5.355 46.223 824 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.92 % Allowed : 21.38 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.32), residues: 719 helix: -2.99 (0.80), residues: 27 sheet: -0.45 (0.36), residues: 224 loop : -1.30 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 273 TYR 0.014 0.001 TYR L 49 PHE 0.022 0.001 PHE N 168 TRP 0.007 0.001 TRP N 64 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6114) covalent geometry : angle 0.64966 ( 8293) SS BOND : bond 0.00432 ( 8) SS BOND : angle 2.96123 ( 16) hydrogen bonds : bond 0.02885 ( 111) hydrogen bonds : angle 6.11396 ( 255) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8050 (tp30) cc_final: 0.7569 (tp30) REVERT: H 67 PHE cc_start: 0.8114 (m-10) cc_final: 0.7892 (m-80) REVERT: R 442 ASP cc_start: 0.8223 (m-30) cc_final: 0.7964 (m-30) REVERT: B 47 TYR cc_start: 0.4891 (OUTLIER) cc_final: 0.4375 (p90) REVERT: B 72 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7270 (mp) REVERT: B 94 ASP cc_start: 0.8040 (t70) cc_final: 0.7826 (t70) REVERT: B 103 LYS cc_start: 0.8303 (tptt) cc_final: 0.8056 (tptm) REVERT: N 43 PHE cc_start: 0.6820 (p90) cc_final: 0.5448 (p90) REVERT: N 190 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.7107 (mmp-170) outliers start: 32 outliers final: 27 residues processed: 188 average time/residue: 0.0867 time to fit residues: 20.5315 Evaluate side-chains 192 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 285 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN ** N 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.117290 restraints weight = 9547.630| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.00 r_work: 0.3375 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6122 Z= 0.180 Angle : 0.677 12.497 8309 Z= 0.355 Chirality : 0.045 0.187 892 Planarity : 0.004 0.045 1058 Dihedral : 5.442 48.870 824 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.77 % Allowed : 21.69 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.32), residues: 719 helix: -2.98 (0.81), residues: 27 sheet: -0.49 (0.36), residues: 224 loop : -1.26 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 273 TYR 0.016 0.001 TYR N 170 PHE 0.016 0.001 PHE N 32 TRP 0.006 0.001 TRP L 35 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6114) covalent geometry : angle 0.66476 ( 8293) SS BOND : bond 0.00485 ( 8) SS BOND : angle 2.96457 ( 16) hydrogen bonds : bond 0.02953 ( 111) hydrogen bonds : angle 6.16169 ( 255) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: H 26 GLU cc_start: 0.8078 (tp30) cc_final: 0.7578 (tp30) REVERT: H 67 PHE cc_start: 0.8169 (m-10) cc_final: 0.7892 (m-80) REVERT: R 442 ASP cc_start: 0.8279 (m-30) cc_final: 0.7976 (m-30) REVERT: B 47 TYR cc_start: 0.4696 (OUTLIER) cc_final: 0.3903 (p90) REVERT: B 72 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7205 (mp) REVERT: N 43 PHE cc_start: 0.6864 (p90) cc_final: 0.5462 (p90) REVERT: N 111 ASP cc_start: 0.7721 (p0) cc_final: 0.7287 (p0) REVERT: N 129 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8137 (ttpt) REVERT: N 168 PHE cc_start: 0.8665 (t80) cc_final: 0.8388 (t80) REVERT: N 190 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7096 (mmp-170) REVERT: N 224 GLU cc_start: 0.7325 (tp30) cc_final: 0.6525 (mm-30) outliers start: 31 outliers final: 28 residues processed: 184 average time/residue: 0.0896 time to fit residues: 20.5887 Evaluate side-chains 196 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 285 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.150277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118913 restraints weight = 9542.506| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.97 r_work: 0.3407 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6122 Z= 0.148 Angle : 0.670 12.103 8309 Z= 0.350 Chirality : 0.044 0.150 892 Planarity : 0.004 0.045 1058 Dihedral : 5.419 51.526 824 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.92 % Allowed : 22.15 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.32), residues: 719 helix: -2.91 (0.83), residues: 27 sheet: -0.41 (0.36), residues: 224 loop : -1.22 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 273 TYR 0.014 0.001 TYR L 49 PHE 0.013 0.001 PHE R 456 TRP 0.005 0.001 TRP R 436 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6114) covalent geometry : angle 0.65951 ( 8293) SS BOND : bond 0.00374 ( 8) SS BOND : angle 2.82333 ( 16) hydrogen bonds : bond 0.02819 ( 111) hydrogen bonds : angle 6.12098 ( 255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.72 seconds wall clock time: 31 minutes 46.23 seconds (1906.23 seconds total)