Starting phenix.real_space_refine on Thu Jul 2 02:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.map" model { file = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2026/7urd_26709.cif" } resolution = 2.92 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= 0.007 sd= 0.087 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 3642 2.51 5 N 897 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'O50': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 56.521 29.274 19.732 1.00108.35 S ATOM 2880 SG CYS A 376 55.636 28.723 23.034 1.00118.02 S ATOM 2908 SG CYS A 380 59.361 29.098 21.112 1.00127.74 S Time building chain proxies: 1.51, per 1000 atoms: 0.27 Number of scatterers: 5534 At special positions: 0 Unit cell: (98.77, 69.72, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 959 8.00 N 897 7.00 C 3642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 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: 0.54 Conformation dependent library (CDL) restraints added in 199.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 506 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 380 " Number of angles added : 3 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 51.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 5 through 28 removed outlier: 4.921A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.952A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.686A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.570A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.842A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.870A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.654A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 292 through 301 removed outlier: 4.359A pdb=" N ASN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.610A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.713A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.891A pdb=" N PHE L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.201A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.740A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 206 Processing sheet with id=AA3, first strand: chain 'L' and resid 24 through 27 removed outlier: 5.677A pdb=" N THR L 89 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.863A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 849 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: 0.83 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.19: 4 1.19 - 1.39: 2353 1.39 - 1.59: 3288 1.59 - 1.78: 10 1.78 - 1.98: 50 Bond restraints: 5705 Sorted by residual: bond pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " ideal model delta sigma weight residual 1.550 1.980 -0.430 2.00e-02 2.50e+03 4.62e+02 bond pdb=" C01 AJP A 504 " pdb=" C02 AJP A 504 " ideal model delta sigma weight residual 1.521 1.947 -0.426 2.00e-02 2.50e+03 4.55e+02 bond pdb=" C08 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.410 0.998 0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" C02 AJP A 504 " pdb=" C03 AJP A 504 " ideal model delta sigma weight residual 1.525 1.133 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" C05 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.407 1.784 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 7706 4.20 - 8.40: 54 8.40 - 12.60: 7 12.60 - 16.80: 4 16.80 - 20.99: 1 Bond angle restraints: 7772 Sorted by residual: angle pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " ideal model delta sigma weight residual 120.30 141.29 -20.99 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C11 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C81 AJP A 504 " ideal model delta sigma weight residual 114.35 98.09 16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sigma weight residual 114.18 129.16 -14.98 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " pdb=" C10 AJP A 504 " ideal model delta sigma weight residual 107.39 93.44 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C PRO A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.47 124.77 -5.30 1.16e+00 7.43e-01 2.09e+01 ... (remaining 7767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.46: 2976 20.46 - 40.93: 195 40.93 - 61.39: 27 61.39 - 81.86: 4 81.86 - 102.32: 3 Dihedral angle restraints: 3205 sinusoidal: 1243 harmonic: 1962 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLY B 210 " pdb=" C GLY B 210 " pdb=" N SER B 211 " pdb=" CA SER B 211 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TYR H 73 " pdb=" C TYR H 73 " pdb=" N TYR H 74 " pdb=" CA TYR H 74 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 3202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.107: 849 1.107 - 2.213: 0 2.213 - 3.320: 0 3.320 - 4.426: 1 4.426 - 5.533: 24 Chirality restraints: 874 Sorted by residual: chirality pdb=" C15 AJP A 504 " pdb=" C14 AJP A 504 " pdb=" C16 AJP A 504 " pdb=" C20 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.42 3.11 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C16 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C17 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C20 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C19 AJP A 504 " pdb=" C21 AJP A 504 " both_signs ideal model delta sigma weight residual False 2.96 -2.42 5.38 2.00e-01 2.50e+01 7.23e+02 ... (remaining 871 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 216 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C LEU A 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 14 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 15 " -0.009 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5456 3.27 - 3.81: 9026 3.81 - 4.36: 11401 4.36 - 4.90: 19866 Nonbonded interactions: 46016 Sorted by model distance: nonbonded pdb=" OG SER A 242 " pdb=" OD1 ASP A 413 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 360 " pdb=" O VAL A 371 " model vdw 2.196 3.120 nonbonded pdb=" OG SER H 26 " pdb=" OG SER H 40 " model vdw 2.251 3.040 nonbonded pdb=" OG SER L 27 " pdb=" OG1 THR L 42 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 79 " pdb=" OH TYR A 160 " model vdw 2.280 3.040 ... (remaining 46011 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: 2.010 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.410 Find NCS groups from input model: 0.020 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.018 0.430 5714 Z= 0.878 Angle : 1.040 30.975 7785 Z= 0.425 Chirality : 0.833 5.533 874 Planarity : 0.004 0.043 924 Dihedral : 13.735 102.322 1936 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.44 (0.28), residues: 666 helix: -0.91 (0.25), residues: 324 sheet: -1.58 (0.42), residues: 129 loop : -2.50 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.013 0.001 TYR A 83 PHE 0.018 0.001 PHE A 403 TRP 0.010 0.001 TRP H 66 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.01739 / 0.86 ( 5705) covalent geometry : angle 0.95385 / 0.41 ( 7772) SS BOND : bond 0.00203 / 0.12 ( 5) SS BOND : angle 0.55958 / 0.35 ( 10) hydrogen bonds : bond 0.11031 / 6.87 ( 298) hydrogen bonds : angle 6.14658 / 4.33 ( 849) metal coordination : bond 0.16255 / 8.28 ( 4) metal coordination : angle 21.12353 / 19.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6938 (mtm180) REVERT: A 361 LYS cc_start: 0.7957 (tttt) cc_final: 0.7605 (ttpt) REVERT: A 432 HIS cc_start: 0.8143 (t-90) cc_final: 0.7735 (t70) REVERT: L 23 HIS cc_start: 0.8141 (m-70) cc_final: 0.7933 (m-70) REVERT: H 101 GLN cc_start: 0.8481 (tt0) cc_final: 0.8253 (tt0) REVERT: H 119 TYR cc_start: 0.6625 (t80) cc_final: 0.6393 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.5645 time to fit residues: 59.4590 Evaluate side-chains 73 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 24 GLN A 66 HIS A 91 HIS A 94 HIS A 174 HIS A 247 HIS L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.127060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.090850 restraints weight = 6369.702| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.29 r_work: 0.2819 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5714 Z= 0.147 Angle : 1.098 31.216 7785 Z= 0.418 Chirality : 0.122 2.127 874 Planarity : 0.004 0.040 924 Dihedral : 6.625 51.327 778 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 10.05 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.69 (0.32), residues: 666 helix: 0.56 (0.27), residues: 329 sheet: -1.02 (0.43), residues: 129 loop : -1.58 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.019 0.001 TYR A 83 PHE 0.016 0.001 PHE A 403 TRP 0.009 0.001 TRP H 66 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 5705) covalent geometry : angle 1.09891 / 0.42 ( 7772) SS BOND : bond 0.00292 / 0.16 ( 5) SS BOND : angle 0.54404 / 0.34 ( 10) hydrogen bonds : bond 0.03100 / 1.94 ( 298) hydrogen bonds : angle 4.43801 / 3.19 ( 849) metal coordination : bond 0.01048 / 0.53 ( 4) metal coordination : angle 1.15841 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7023 (mmt) cc_final: 0.6319 (mtm) REVERT: A 124 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7210 (mtm-85) REVERT: A 142 ASP cc_start: 0.8511 (m-30) cc_final: 0.8198 (m-30) REVERT: A 154 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: A 235 ARG cc_start: 0.7441 (mmt180) cc_final: 0.6632 (mtm180) REVERT: A 270 GLU cc_start: 0.8301 (pt0) cc_final: 0.7989 (pt0) REVERT: A 361 LYS cc_start: 0.7658 (tttt) cc_final: 0.7370 (ttpt) REVERT: A 375 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7794 (mtt-85) REVERT: A 432 HIS cc_start: 0.7879 (t-90) cc_final: 0.7451 (t70) REVERT: L 23 HIS cc_start: 0.8306 (m-70) cc_final: 0.8012 (m-70) REVERT: H 101 GLN cc_start: 0.8209 (tt0) cc_final: 0.7944 (tt0) REVERT: H 119 TYR cc_start: 0.6831 (t80) cc_final: 0.6479 (t80) outliers start: 11 outliers final: 2 residues processed: 92 average time/residue: 0.5450 time to fit residues: 52.2846 Evaluate side-chains 86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092188 restraints weight = 6292.655| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.28 r_work: 0.2835 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5714 Z= 0.117 Angle : 1.060 30.735 7785 Z= 0.398 Chirality : 0.122 2.108 874 Planarity : 0.004 0.039 924 Dihedral : 6.137 48.358 778 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.91 % Allowed : 13.52 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.21 (0.33), residues: 666 helix: 1.34 (0.28), residues: 329 sheet: -0.76 (0.43), residues: 129 loop : -1.12 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.017 0.001 TYR A 83 PHE 0.013 0.001 PHE A 403 TRP 0.007 0.001 TRP A 74 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5705) covalent geometry : angle 1.05980 / 0.40 ( 7772) SS BOND : bond 0.00393 / 0.20 ( 5) SS BOND : angle 0.61460 / 0.38 ( 10) hydrogen bonds : bond 0.02718 / 1.72 ( 298) hydrogen bonds : angle 4.03356 / 2.91 ( 849) metal coordination : bond 0.00454 / 0.23 ( 4) metal coordination : angle 1.41953 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7076 (mmt) cc_final: 0.6325 (mtm) REVERT: A 112 MET cc_start: 0.7894 (mtp) cc_final: 0.7687 (mtp) REVERT: A 124 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7154 (mtt-85) REVERT: A 154 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 235 ARG cc_start: 0.7491 (mmt180) cc_final: 0.6724 (mtm180) REVERT: A 375 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: A 432 HIS cc_start: 0.7901 (t-90) cc_final: 0.7621 (t-170) REVERT: L 81 ARG cc_start: 0.7928 (ptp90) cc_final: 0.7711 (ptp-170) REVERT: H 101 GLN cc_start: 0.8292 (tt0) cc_final: 0.8069 (tt0) REVERT: H 119 TYR cc_start: 0.6789 (t80) cc_final: 0.6488 (t80) outliers start: 11 outliers final: 2 residues processed: 90 average time/residue: 0.5487 time to fit residues: 51.4919 Evaluate side-chains 83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093768 restraints weight = 6141.700| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.32 r_work: 0.2883 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5714 Z= 0.118 Angle : 1.058 30.817 7785 Z= 0.397 Chirality : 0.122 2.114 874 Planarity : 0.004 0.039 924 Dihedral : 6.011 47.122 778 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.08 % Allowed : 15.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.61 (0.34), residues: 666 helix: 1.63 (0.29), residues: 331 sheet: -0.50 (0.44), residues: 127 loop : -0.93 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.017 0.001 TYR A 83 PHE 0.013 0.001 PHE A 403 TRP 0.006 0.001 TRP A 74 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 5705) covalent geometry : angle 1.05866 / 0.40 ( 7772) SS BOND : bond 0.00337 / 0.18 ( 5) SS BOND : angle 0.69062 / 0.42 ( 10) hydrogen bonds : bond 0.02669 / 1.71 ( 298) hydrogen bonds : angle 3.92975 / 2.84 ( 849) metal coordination : bond 0.00525 / 0.26 ( 4) metal coordination : angle 1.24828 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7639 (ptt) REVERT: A 109 MET cc_start: 0.6967 (mmt) cc_final: 0.6241 (mtm) REVERT: A 112 MET cc_start: 0.7806 (mtp) cc_final: 0.7437 (mtt) REVERT: A 122 LYS cc_start: 0.8228 (tttm) cc_final: 0.7994 (tttp) REVERT: A 124 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7067 (mtt-85) REVERT: A 154 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: A 235 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6582 (mtm180) REVERT: A 338 PHE cc_start: 0.7384 (t80) cc_final: 0.6387 (m-80) REVERT: A 375 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7820 (mtt-85) REVERT: A 427 MET cc_start: 0.7231 (ttp) cc_final: 0.6831 (ttt) REVERT: A 432 HIS cc_start: 0.7820 (t-90) cc_final: 0.7441 (t-170) REVERT: L 89 THR cc_start: 0.8845 (p) cc_final: 0.8173 (m) REVERT: H 29 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6546 (mt-10) REVERT: H 101 GLN cc_start: 0.8196 (tt0) cc_final: 0.7953 (tt0) REVERT: H 119 TYR cc_start: 0.6748 (t80) cc_final: 0.6402 (t80) outliers start: 12 outliers final: 3 residues processed: 90 average time/residue: 0.4931 time to fit residues: 46.4332 Evaluate side-chains 87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091791 restraints weight = 6391.988| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.36 r_work: 0.2853 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5714 Z= 0.150 Angle : 1.068 30.498 7785 Z= 0.404 Chirality : 0.123 2.112 874 Planarity : 0.004 0.039 924 Dihedral : 6.124 47.849 778 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.56 % Allowed : 16.64 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.75 (0.34), residues: 666 helix: 1.73 (0.29), residues: 329 sheet: -0.34 (0.45), residues: 127 loop : -0.88 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.018 0.001 TYR A 83 PHE 0.016 0.001 PHE A 403 TRP 0.007 0.001 TRP H 66 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 5705) covalent geometry : angle 1.06799 / 0.40 ( 7772) SS BOND : bond 0.00284 / 0.14 ( 5) SS BOND : angle 0.78616 / 0.47 ( 10) hydrogen bonds : bond 0.02800 / 1.81 ( 298) hydrogen bonds : angle 3.94029 / 2.85 ( 849) metal coordination : bond 0.00817 / 0.41 ( 4) metal coordination : angle 1.66968 / 1.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6977 (mmt) cc_final: 0.6242 (mtm) REVERT: A 124 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: A 154 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: A 235 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6558 (mtm180) REVERT: A 427 MET cc_start: 0.7191 (ttp) cc_final: 0.6849 (ttt) REVERT: A 432 HIS cc_start: 0.7819 (t-90) cc_final: 0.7525 (t-170) REVERT: L 89 THR cc_start: 0.8831 (p) cc_final: 0.8144 (m) REVERT: H 101 GLN cc_start: 0.8206 (tt0) cc_final: 0.7997 (tt0) REVERT: H 119 TYR cc_start: 0.6821 (t80) cc_final: 0.6427 (t80) outliers start: 9 outliers final: 3 residues processed: 85 average time/residue: 0.5421 time to fit residues: 48.0506 Evaluate side-chains 85 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.092857 restraints weight = 6251.395| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.33 r_work: 0.2871 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5714 Z= 0.127 Angle : 1.059 30.526 7785 Z= 0.398 Chirality : 0.122 2.110 874 Planarity : 0.004 0.039 924 Dihedral : 6.014 47.011 778 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 16.46 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.92 (0.34), residues: 666 helix: 1.83 (0.29), residues: 330 sheet: -0.21 (0.46), residues: 127 loop : -0.79 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.017 0.001 TYR A 83 PHE 0.014 0.001 PHE A 403 TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5705) covalent geometry : angle 1.05926 / 0.40 ( 7772) SS BOND : bond 0.00218 / 0.12 ( 5) SS BOND : angle 0.78298 / 0.47 ( 10) hydrogen bonds : bond 0.02657 / 1.72 ( 298) hydrogen bonds : angle 3.83074 / 2.77 ( 849) metal coordination : bond 0.00637 / 0.32 ( 4) metal coordination : angle 1.51381 / 1.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: A 72 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7679 (ptt) REVERT: A 109 MET cc_start: 0.6992 (mmt) cc_final: 0.6239 (mtm) REVERT: A 112 MET cc_start: 0.7792 (mtp) cc_final: 0.7353 (mtt) REVERT: A 124 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7171 (mtm-85) REVERT: A 154 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: A 235 ARG cc_start: 0.7321 (mmt180) cc_final: 0.6588 (mtm180) REVERT: A 427 MET cc_start: 0.7103 (ttp) cc_final: 0.6776 (ttt) REVERT: A 432 HIS cc_start: 0.7835 (t-90) cc_final: 0.7396 (t70) REVERT: L 23 HIS cc_start: 0.8271 (m-70) cc_final: 0.7932 (m-70) REVERT: L 89 THR cc_start: 0.8798 (p) cc_final: 0.8173 (m) REVERT: H 74 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7104 (p90) REVERT: H 101 GLN cc_start: 0.8214 (tt0) cc_final: 0.7980 (tt0) REVERT: H 119 TYR cc_start: 0.6857 (t80) cc_final: 0.6430 (t80) outliers start: 13 outliers final: 4 residues processed: 83 average time/residue: 0.5700 time to fit residues: 49.4501 Evaluate side-chains 85 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.092596 restraints weight = 6376.217| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.34 r_work: 0.2890 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5714 Z= 0.133 Angle : 1.061 30.386 7785 Z= 0.399 Chirality : 0.123 2.109 874 Planarity : 0.004 0.040 924 Dihedral : 6.010 46.911 778 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.91 % Allowed : 17.33 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.02 (0.34), residues: 666 helix: 1.88 (0.29), residues: 330 sheet: -0.07 (0.46), residues: 127 loop : -0.74 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 83 PHE 0.014 0.001 PHE A 403 TRP 0.007 0.001 TRP H 128 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5705) covalent geometry : angle 1.06107 / 0.40 ( 7772) SS BOND : bond 0.00236 / 0.12 ( 5) SS BOND : angle 0.74479 / 0.44 ( 10) hydrogen bonds : bond 0.02664 / 1.72 ( 298) hydrogen bonds : angle 3.80325 / 2.74 ( 849) metal coordination : bond 0.00678 / 0.34 ( 4) metal coordination : angle 1.44128 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7572 (m-30) REVERT: A 72 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7681 (ptt) REVERT: A 109 MET cc_start: 0.6950 (mmt) cc_final: 0.6203 (mtm) REVERT: A 112 MET cc_start: 0.7737 (mtp) cc_final: 0.7296 (mtt) REVERT: A 124 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7132 (mtm-85) REVERT: A 142 ASP cc_start: 0.8301 (m-30) cc_final: 0.7991 (m-30) REVERT: A 154 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 235 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6603 (mtm180) REVERT: A 427 MET cc_start: 0.7143 (ttp) cc_final: 0.6880 (ttt) REVERT: A 432 HIS cc_start: 0.7822 (t-90) cc_final: 0.7374 (t70) REVERT: L 23 HIS cc_start: 0.8225 (m-70) cc_final: 0.7893 (m-70) REVERT: L 89 THR cc_start: 0.8791 (p) cc_final: 0.8178 (m) REVERT: H 74 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6985 (p90) REVERT: H 101 GLN cc_start: 0.8206 (tt0) cc_final: 0.7976 (tt0) REVERT: H 119 TYR cc_start: 0.6932 (t80) cc_final: 0.6494 (t80) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 0.5306 time to fit residues: 47.6705 Evaluate side-chains 90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092445 restraints weight = 6220.282| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.32 r_work: 0.2866 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5714 Z= 0.133 Angle : 1.062 30.341 7785 Z= 0.400 Chirality : 0.122 2.109 874 Planarity : 0.004 0.040 924 Dihedral : 6.006 47.040 778 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.25 % Allowed : 17.16 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.08 (0.34), residues: 666 helix: 1.89 (0.29), residues: 330 sheet: -0.00 (0.46), residues: 127 loop : -0.68 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 83 PHE 0.014 0.001 PHE A 403 TRP 0.008 0.001 TRP H 128 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5705) covalent geometry : angle 1.06236 / 0.40 ( 7772) SS BOND : bond 0.00267 / 0.13 ( 5) SS BOND : angle 0.80472 / 0.49 ( 10) hydrogen bonds : bond 0.02675 / 1.72 ( 298) hydrogen bonds : angle 3.81184 / 2.75 ( 849) metal coordination : bond 0.00668 / 0.34 ( 4) metal coordination : angle 1.40945 / 1.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 72 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7614 (ptt) REVERT: A 109 MET cc_start: 0.6922 (mmt) cc_final: 0.6179 (mtm) REVERT: A 112 MET cc_start: 0.7906 (mtp) cc_final: 0.7458 (mtt) REVERT: A 124 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7110 (mtm-85) REVERT: A 142 ASP cc_start: 0.8266 (m-30) cc_final: 0.7857 (m-30) REVERT: A 154 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: A 235 ARG cc_start: 0.7308 (mmt180) cc_final: 0.6605 (mtm180) REVERT: A 258 GLU cc_start: 0.7867 (tt0) cc_final: 0.7497 (tt0) REVERT: A 427 MET cc_start: 0.7106 (ttp) cc_final: 0.6853 (ttt) REVERT: A 432 HIS cc_start: 0.7798 (t-90) cc_final: 0.7334 (t70) REVERT: L 23 HIS cc_start: 0.8219 (m-70) cc_final: 0.7902 (m-70) REVERT: L 89 THR cc_start: 0.8803 (p) cc_final: 0.8208 (m) REVERT: H 74 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6888 (p90) REVERT: H 101 GLN cc_start: 0.8206 (tt0) cc_final: 0.7998 (tt0) REVERT: H 119 TYR cc_start: 0.6933 (t80) cc_final: 0.6585 (t80) outliers start: 13 outliers final: 4 residues processed: 85 average time/residue: 0.5104 time to fit residues: 45.3013 Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092882 restraints weight = 6272.324| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.29 r_work: 0.2871 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5714 Z= 0.133 Angle : 1.064 30.410 7785 Z= 0.400 Chirality : 0.123 2.108 874 Planarity : 0.004 0.040 924 Dihedral : 5.996 47.212 778 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.73 % Allowed : 17.85 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.09 (0.34), residues: 666 helix: 1.89 (0.29), residues: 331 sheet: 0.06 (0.46), residues: 127 loop : -0.71 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.018 0.001 TYR A 83 PHE 0.014 0.001 PHE A 403 TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 5705) covalent geometry : angle 1.06393 / 0.40 ( 7772) SS BOND : bond 0.00267 / 0.13 ( 5) SS BOND : angle 0.83684 / 0.50 ( 10) hydrogen bonds : bond 0.02688 / 1.72 ( 298) hydrogen bonds : angle 3.79397 / 2.74 ( 849) metal coordination : bond 0.00690 / 0.35 ( 4) metal coordination : angle 1.42287 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 72 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7615 (ptt) REVERT: A 109 MET cc_start: 0.6920 (mmt) cc_final: 0.6216 (mtm) REVERT: A 112 MET cc_start: 0.7870 (mtp) cc_final: 0.7414 (mtt) REVERT: A 124 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7074 (mtm-85) REVERT: A 142 ASP cc_start: 0.8240 (m-30) cc_final: 0.7773 (m-30) REVERT: A 154 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 235 ARG cc_start: 0.7324 (mmt180) cc_final: 0.6593 (mtm180) REVERT: A 258 GLU cc_start: 0.7847 (tt0) cc_final: 0.7492 (tt0) REVERT: A 427 MET cc_start: 0.7044 (ttp) cc_final: 0.6839 (ttt) REVERT: A 432 HIS cc_start: 0.7769 (t-90) cc_final: 0.7319 (t70) REVERT: L 23 HIS cc_start: 0.8186 (m-70) cc_final: 0.7801 (m-70) REVERT: L 89 THR cc_start: 0.8803 (p) cc_final: 0.8204 (m) REVERT: H 74 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6899 (p90) REVERT: H 101 GLN cc_start: 0.8196 (tt0) cc_final: 0.7986 (tt0) REVERT: H 119 TYR cc_start: 0.6916 (t80) cc_final: 0.6572 (t80) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.5218 time to fit residues: 45.3216 Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 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 = 0.3475 r_free = 0.3475 target = 0.129928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093407 restraints weight = 6285.317| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.36 r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5714 Z= 0.116 Angle : 1.059 30.369 7785 Z= 0.396 Chirality : 0.122 2.108 874 Planarity : 0.004 0.040 924 Dihedral : 5.900 46.904 778 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.56 % Allowed : 18.20 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.15 (0.34), residues: 666 helix: 1.94 (0.29), residues: 331 sheet: 0.09 (0.46), residues: 127 loop : -0.69 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.018 0.001 TYR A 83 PHE 0.012 0.001 PHE A 403 TRP 0.008 0.001 TRP H 128 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5705) covalent geometry : angle 1.05867 / 0.40 ( 7772) SS BOND : bond 0.00239 / 0.13 ( 5) SS BOND : angle 0.79904 / 0.48 ( 10) hydrogen bonds : bond 0.02578 / 1.66 ( 298) hydrogen bonds : angle 3.74338 / 2.70 ( 849) metal coordination : bond 0.00571 / 0.29 ( 4) metal coordination : angle 1.35977 / 1.35 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: A 72 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7611 (ptt) REVERT: A 109 MET cc_start: 0.6877 (mmt) cc_final: 0.6186 (mtm) REVERT: A 112 MET cc_start: 0.7851 (mtp) cc_final: 0.7466 (mtt) REVERT: A 124 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7084 (mtm-85) REVERT: A 142 ASP cc_start: 0.8227 (m-30) cc_final: 0.7960 (m-30) REVERT: A 154 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 235 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6601 (mtm180) REVERT: A 427 MET cc_start: 0.7001 (ttp) cc_final: 0.6773 (ttt) REVERT: A 432 HIS cc_start: 0.7750 (t-90) cc_final: 0.7288 (t70) REVERT: L 23 HIS cc_start: 0.8227 (m-70) cc_final: 0.7711 (m-70) REVERT: L 89 THR cc_start: 0.8806 (p) cc_final: 0.8231 (m) REVERT: H 74 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7017 (p90) REVERT: H 101 GLN cc_start: 0.8216 (tt0) cc_final: 0.7982 (tt0) REVERT: H 119 TYR cc_start: 0.6899 (t80) cc_final: 0.6552 (t80) outliers start: 9 outliers final: 4 residues processed: 86 average time/residue: 0.5602 time to fit residues: 50.4325 Evaluate side-chains 89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092749 restraints weight = 6268.146| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.32 r_work: 0.2889 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5714 Z= 0.141 Angle : 1.069 30.209 7785 Z= 0.403 Chirality : 0.123 2.108 874 Planarity : 0.004 0.040 924 Dihedral : 5.999 46.658 778 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.73 % Allowed : 18.37 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.15 (0.34), residues: 666 helix: 1.92 (0.29), residues: 331 sheet: 0.15 (0.47), residues: 127 loop : -0.68 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.018 0.001 TYR A 83 PHE 0.017 0.001 PHE A 62 TRP 0.008 0.001 TRP H 128 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5705) covalent geometry : angle 1.06861 / 0.40 ( 7772) SS BOND : bond 0.00233 / 0.12 ( 5) SS BOND : angle 0.84302 / 0.50 ( 10) hydrogen bonds : bond 0.02709 / 1.75 ( 298) hydrogen bonds : angle 3.80627 / 2.75 ( 849) metal coordination : bond 0.00749 / 0.38 ( 4) metal coordination : angle 1.43994 / 1.43 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.68 seconds wall clock time: 34 minutes 54.02 seconds (2094.02 seconds total)