Starting phenix.real_space_refine on Sun Apr 5 02:08:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lz2_63521/04_2026/9lz2_63521.map" } resolution = 3.0 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= 0.001 sd= 0.021 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 P 6 5.49 5 S 31 5.16 5 C 4583 2.51 5 N 1196 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7117 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2778 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 321} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "R" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2331 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 1.81, per 1000 atoms: 0.25 Number of scatterers: 7117 At special positions: 0 Unit cell: (78.12, 103.23, 161.82, 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) S 31 16.00 P 6 15.00 O 1301 8.00 N 1196 7.00 C 4583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 0.69 Conformation dependent library (CDL) restraints added in 244.0 milliseconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 32.7% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'R' and resid 179 through 212 Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.560A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 360 through 392 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 450 Processing helix chain 'R' and resid 450 through 460 Processing helix chain 'R' and resid 463 through 481 removed outlier: 3.777A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 115 removed outlier: 3.641A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.730A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 141 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.730A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.967A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.967A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 15 removed outlier: 8.540A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.561A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.584A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1116 1.31 - 1.44: 2053 1.44 - 1.57: 4051 1.57 - 1.70: 23 1.70 - 1.82: 45 Bond restraints: 7288 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" OG1 TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CA GLN A 248 " pdb=" C GLN A 248 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.23e-02 6.61e+03 1.84e+01 bond pdb=" CA VAL A 34 " pdb=" C VAL A 34 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.75e+01 bond pdb=" O3P TPO R1359 " pdb=" P TPO R1359 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 7283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 9742 2.52 - 5.04: 126 5.04 - 7.56: 17 7.56 - 10.08: 7 10.08 - 12.60: 3 Bond angle restraints: 9895 Sorted by residual: angle pdb=" N MET R 312 " pdb=" CA MET R 312 " pdb=" C MET R 312 " ideal model delta sigma weight residual 112.87 122.54 -9.67 1.20e+00 6.94e-01 6.49e+01 angle pdb=" CA PRO A 120 " pdb=" N PRO A 120 " pdb=" CD PRO A 120 " ideal model delta sigma weight residual 112.00 103.28 8.72 1.40e+00 5.10e-01 3.88e+01 angle pdb=" O LEU A 33 " pdb=" C LEU A 33 " pdb=" N VAL A 34 " ideal model delta sigma weight residual 123.48 117.59 5.89 1.14e+00 7.69e-01 2.67e+01 angle pdb=" N ILE R 458 " pdb=" CA ILE R 458 " pdb=" C ILE R 458 " ideal model delta sigma weight residual 110.36 115.58 -5.22 1.05e+00 9.07e-01 2.47e+01 angle pdb=" C SER R 316 " pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 122.53 113.47 9.06 1.92e+00 2.71e-01 2.23e+01 ... (remaining 9890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4021 17.82 - 35.63: 245 35.63 - 53.45: 46 53.45 - 71.27: 13 71.27 - 89.09: 4 Dihedral angle restraints: 4329 sinusoidal: 1717 harmonic: 2612 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual -86.00 -19.26 -66.74 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N LEU A 300 " pdb=" CA LEU A 300 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE A 314 " pdb=" C ILE A 314 " pdb=" N LEU A 315 " pdb=" CA LEU A 315 " ideal model delta harmonic sigma weight residual 180.00 -153.59 -26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 4326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1050 0.101 - 0.201: 60 0.201 - 0.302: 0 0.302 - 0.402: 0 0.402 - 0.503: 1 Chirality restraints: 1111 Sorted by residual: chirality pdb=" CA MET R 312 " pdb=" N MET R 312 " pdb=" C MET R 312 " pdb=" CB MET R 312 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA GLU R 444 " pdb=" N GLU R 444 " pdb=" C GLU R 444 " pdb=" CB GLU R 444 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA PRO A 120 " pdb=" N PRO A 120 " pdb=" C PRO A 120 " pdb=" CB PRO A 120 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.22e-01 ... (remaining 1108 not shown) Planarity restraints: 1230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 33 " 0.024 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C LEU A 33 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU A 33 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL A 34 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 119 " 0.072 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 120 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 130 " -0.061 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO A 131 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.050 5.00e-02 4.00e+02 ... (remaining 1227 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 55 2.56 - 3.14: 5494 3.14 - 3.73: 10961 3.73 - 4.31: 15260 4.31 - 4.90: 26037 Nonbonded interactions: 57807 Sorted by model distance: nonbonded pdb=" O VAL R 412 " pdb=" OH TYR R 459 " model vdw 1.970 3.040 nonbonded pdb=" OD2 ASP A 260 " pdb=" OH TYR A 272 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASP A 204 " pdb=" OH TYR A 208 " model vdw 2.197 3.040 nonbonded pdb=" O MET R 445 " pdb=" OG SER R 449 " model vdw 2.223 3.040 nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 102 " model vdw 2.228 3.040 ... (remaining 57802 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.160 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.006 0.110 7291 Z= 0.309 Angle : 0.753 12.598 9901 Z= 0.415 Chirality : 0.049 0.503 1111 Planarity : 0.007 0.104 1230 Dihedral : 12.618 89.087 2636 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 2.90 % Favored : 96.87 % Rotamer: Outliers : 0.39 % Allowed : 0.65 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.77 (0.30), residues: 863 helix: 1.72 (0.33), residues: 262 sheet: 0.24 (0.36), residues: 238 loop : -0.10 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 282 TYR 0.032 0.002 TYR R 191 PHE 0.022 0.002 PHE R 375 TRP 0.011 0.001 TRP R 361 HIS 0.008 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 7288) covalent geometry : angle 0.74850 ( 9895) SS BOND : bond 0.00550 ( 3) SS BOND : angle 3.29095 ( 6) hydrogen bonds : bond 0.16214 ( 379) hydrogen bonds : angle 7.67451 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6488 (ttp80) REVERT: A 29 ASP cc_start: 0.7179 (t70) cc_final: 0.6808 (t70) REVERT: A 122 ASN cc_start: 0.7664 (t0) cc_final: 0.7324 (t0) REVERT: A 232 LYS cc_start: 0.7762 (ttmm) cc_final: 0.6984 (ttmm) REVERT: A 257 GLU cc_start: 0.6828 (tt0) cc_final: 0.6308 (tt0) REVERT: H 111 ASP cc_start: 0.7215 (m-30) cc_final: 0.6975 (m-30) REVERT: R 231 MET cc_start: 0.7434 (mtm) cc_final: 0.7224 (mtp) REVERT: R 304 LEU cc_start: 0.7806 (mt) cc_final: 0.7490 (mt) REVERT: R 306 LEU cc_start: 0.8164 (tp) cc_final: 0.7897 (tm) REVERT: R 373 LEU cc_start: 0.8075 (tp) cc_final: 0.7865 (tm) REVERT: R 379 ILE cc_start: 0.8379 (mt) cc_final: 0.8135 (mp) REVERT: R 446 LEU cc_start: 0.7974 (tp) cc_final: 0.7771 (tm) outliers start: 3 outliers final: 1 residues processed: 190 average time/residue: 0.5039 time to fit residues: 101.4249 Evaluate side-chains 185 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 219 HIS A 223 ASN A 225 ASN H 87 ASN R 216 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.144502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.123644 restraints weight = 10335.502| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.41 r_work: 0.3507 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7291 Z= 0.217 Angle : 0.615 7.284 9901 Z= 0.328 Chirality : 0.044 0.171 1111 Planarity : 0.005 0.063 1230 Dihedral : 6.180 79.687 991 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 1.17 % Allowed : 9.62 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.88 (0.29), residues: 863 helix: 1.75 (0.33), residues: 263 sheet: 0.37 (0.35), residues: 235 loop : -0.04 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 51 TYR 0.026 0.002 TYR R 191 PHE 0.019 0.002 PHE R 335 TRP 0.022 0.002 TRP R 474 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 7288) covalent geometry : angle 0.61274 ( 9895) SS BOND : bond 0.00637 ( 3) SS BOND : angle 2.23103 ( 6) hydrogen bonds : bond 0.04438 ( 379) hydrogen bonds : angle 5.40003 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7272 (ttp80) cc_final: 0.7023 (ttp80) REVERT: A 17 LYS cc_start: 0.8169 (tppp) cc_final: 0.7457 (tppp) REVERT: A 29 ASP cc_start: 0.7586 (t70) cc_final: 0.7312 (t0) REVERT: A 54 TYR cc_start: 0.7597 (m-80) cc_final: 0.7388 (m-80) REVERT: A 62 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7065 (mtt90) REVERT: A 122 ASN cc_start: 0.8170 (t0) cc_final: 0.7823 (t0) REVERT: A 129 LEU cc_start: 0.8733 (mt) cc_final: 0.8530 (mp) REVERT: A 143 ASP cc_start: 0.8122 (p0) cc_final: 0.7383 (p0) REVERT: A 232 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7899 (ttmm) REVERT: A 250 LYS cc_start: 0.8300 (mttt) cc_final: 0.8095 (mttt) REVERT: H 28 SER cc_start: 0.8407 (t) cc_final: 0.8116 (m) REVERT: H 46 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7769 (mmpt) REVERT: H 63 TYR cc_start: 0.8416 (m-80) cc_final: 0.8132 (m-80) REVERT: H 111 ASP cc_start: 0.7542 (m-30) cc_final: 0.7299 (m-30) REVERT: R 231 MET cc_start: 0.8063 (mtm) cc_final: 0.7859 (mtp) REVERT: R 233 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.5797 (ptp-170) REVERT: R 290 TYR cc_start: 0.7465 (t80) cc_final: 0.7205 (t80) REVERT: R 379 ILE cc_start: 0.8378 (mt) cc_final: 0.8176 (mm) REVERT: R 446 LEU cc_start: 0.7970 (tp) cc_final: 0.7767 (tm) REVERT: R 451 GLN cc_start: 0.7697 (tp40) cc_final: 0.7400 (tp40) outliers start: 9 outliers final: 4 residues processed: 198 average time/residue: 0.5134 time to fit residues: 107.4882 Evaluate side-chains 196 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 457 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 153 ASN A 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.123179 restraints weight = 10287.994| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.34 r_work: 0.3501 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7291 Z= 0.208 Angle : 0.579 6.118 9901 Z= 0.309 Chirality : 0.043 0.165 1111 Planarity : 0.005 0.052 1230 Dihedral : 6.132 77.676 989 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 3.25 % Allowed : 12.74 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.93 (0.29), residues: 863 helix: 1.94 (0.33), residues: 260 sheet: 0.33 (0.34), residues: 243 loop : -0.06 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 282 TYR 0.024 0.002 TYR R 191 PHE 0.017 0.001 PHE R 335 TRP 0.011 0.001 TRP R 474 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7288) covalent geometry : angle 0.57795 ( 9895) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.31625 ( 6) hydrogen bonds : bond 0.04071 ( 379) hydrogen bonds : angle 5.06681 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7339 (ttp80) REVERT: A 17 LYS cc_start: 0.7964 (tppp) cc_final: 0.7658 (tppp) REVERT: A 29 ASP cc_start: 0.7804 (t70) cc_final: 0.7547 (t0) REVERT: A 44 ASP cc_start: 0.7317 (p0) cc_final: 0.7007 (p0) REVERT: A 62 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7629 (mtt90) REVERT: A 122 ASN cc_start: 0.8362 (t0) cc_final: 0.8055 (t0) REVERT: A 143 ASP cc_start: 0.8348 (p0) cc_final: 0.8082 (p0) REVERT: A 250 LYS cc_start: 0.8511 (mttt) cc_final: 0.8303 (mttt) REVERT: A 318 ILE cc_start: 0.8434 (mm) cc_final: 0.8217 (mt) REVERT: H 28 SER cc_start: 0.8425 (t) cc_final: 0.8145 (m) REVERT: H 46 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7869 (mmpt) REVERT: H 63 TYR cc_start: 0.8524 (m-80) cc_final: 0.8292 (m-80) REVERT: H 111 ASP cc_start: 0.7772 (m-30) cc_final: 0.7520 (m-30) REVERT: R 290 TYR cc_start: 0.7672 (t80) cc_final: 0.7462 (t80) outliers start: 25 outliers final: 9 residues processed: 203 average time/residue: 0.4989 time to fit residues: 107.4510 Evaluate side-chains 206 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain R residue 427 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 153 ASN A 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122125 restraints weight = 10387.527| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.34 r_work: 0.3489 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7291 Z= 0.228 Angle : 0.603 9.423 9901 Z= 0.317 Chirality : 0.044 0.163 1111 Planarity : 0.005 0.048 1230 Dihedral : 6.233 76.531 989 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 15.47 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.85 (0.29), residues: 863 helix: 1.77 (0.32), residues: 259 sheet: 0.33 (0.34), residues: 243 loop : -0.05 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.023 0.002 TYR R 191 PHE 0.021 0.002 PHE A 149 TRP 0.010 0.002 TRP R 474 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 7288) covalent geometry : angle 0.59740 ( 9895) SS BOND : bond 0.01004 ( 3) SS BOND : angle 3.27667 ( 6) hydrogen bonds : bond 0.04023 ( 379) hydrogen bonds : angle 4.99407 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7322 (ttp80) REVERT: A 17 LYS cc_start: 0.8062 (tppp) cc_final: 0.7831 (tppp) REVERT: A 29 ASP cc_start: 0.7835 (t70) cc_final: 0.7590 (t0) REVERT: A 44 ASP cc_start: 0.7397 (p0) cc_final: 0.7067 (p0) REVERT: A 62 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7738 (mtt90) REVERT: A 122 ASN cc_start: 0.8347 (t0) cc_final: 0.8076 (t0) REVERT: A 172 GLN cc_start: 0.8677 (mt0) cc_final: 0.8462 (tt0) REVERT: A 230 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8453 (ttpp) REVERT: A 270 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7821 (ttpt) REVERT: H 28 SER cc_start: 0.8399 (t) cc_final: 0.8152 (m) REVERT: H 46 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7892 (mmpt) REVERT: H 111 ASP cc_start: 0.7751 (m-30) cc_final: 0.7526 (m-30) REVERT: R 233 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.5361 (ptp-170) REVERT: R 237 ILE cc_start: 0.7329 (tt) cc_final: 0.7118 (tt) REVERT: R 312 MET cc_start: 0.7289 (mmm) cc_final: 0.6968 (mtp) outliers start: 16 outliers final: 13 residues processed: 210 average time/residue: 0.5072 time to fit residues: 112.9431 Evaluate side-chains 210 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 419 VAL Chi-restraints excluded: chain R residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 153 ASN A 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128205 restraints weight = 10480.988| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.38 r_work: 0.3505 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7291 Z= 0.155 Angle : 0.560 7.657 9901 Z= 0.296 Chirality : 0.043 0.192 1111 Planarity : 0.004 0.045 1230 Dihedral : 6.129 76.509 989 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 3.25 % Allowed : 16.38 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.94 (0.29), residues: 863 helix: 1.83 (0.32), residues: 262 sheet: 0.34 (0.34), residues: 244 loop : 0.03 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 282 TYR 0.024 0.002 TYR R 191 PHE 0.016 0.001 PHE A 149 TRP 0.011 0.001 TRP R 352 HIS 0.004 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7288) covalent geometry : angle 0.55616 ( 9895) SS BOND : bond 0.00739 ( 3) SS BOND : angle 2.57512 ( 6) hydrogen bonds : bond 0.03747 ( 379) hydrogen bonds : angle 4.78730 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7079 (ttp80) REVERT: A 10 LYS cc_start: 0.8330 (ptmm) cc_final: 0.8099 (pttp) REVERT: A 17 LYS cc_start: 0.7997 (tppp) cc_final: 0.7761 (tppp) REVERT: A 29 ASP cc_start: 0.7624 (t70) cc_final: 0.7339 (t0) REVERT: A 44 ASP cc_start: 0.7130 (p0) cc_final: 0.6721 (p0) REVERT: A 62 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7251 (mtt90) REVERT: A 76 ARG cc_start: 0.6828 (ttt-90) cc_final: 0.6566 (ttt-90) REVERT: A 78 ASP cc_start: 0.7439 (m-30) cc_final: 0.6883 (m-30) REVERT: A 122 ASN cc_start: 0.8166 (t0) cc_final: 0.7891 (t0) REVERT: A 230 LYS cc_start: 0.8517 (ttpp) cc_final: 0.8264 (ttpp) REVERT: A 270 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7537 (ttpt) REVERT: H 28 SER cc_start: 0.8311 (t) cc_final: 0.8110 (m) REVERT: H 46 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7761 (mmpt) REVERT: H 111 ASP cc_start: 0.7567 (m-30) cc_final: 0.7351 (m-30) REVERT: R 221 TYR cc_start: 0.8034 (m-80) cc_final: 0.7781 (m-80) REVERT: R 233 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.5327 (ptp-170) REVERT: R 310 ILE cc_start: 0.8764 (mt) cc_final: 0.8552 (mt) REVERT: R 312 MET cc_start: 0.6967 (mmm) cc_final: 0.6724 (mtp) outliers start: 25 outliers final: 12 residues processed: 206 average time/residue: 0.5237 time to fit residues: 114.1028 Evaluate side-chains 206 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 153 ASN A 223 ASN A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.122406 restraints weight = 10352.283| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.36 r_work: 0.3494 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7291 Z= 0.185 Angle : 0.570 8.911 9901 Z= 0.300 Chirality : 0.043 0.220 1111 Planarity : 0.005 0.046 1230 Dihedral : 6.114 76.812 989 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.01 % Favored : 96.87 % Rotamer: Outliers : 2.86 % Allowed : 17.04 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.91 (0.29), residues: 863 helix: 1.83 (0.32), residues: 262 sheet: 0.31 (0.34), residues: 244 loop : 0.00 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 282 TYR 0.024 0.002 TYR R 191 PHE 0.022 0.002 PHE R 375 TRP 0.008 0.001 TRP R 474 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7288) covalent geometry : angle 0.56801 ( 9895) SS BOND : bond 0.00513 ( 3) SS BOND : angle 2.17745 ( 6) hydrogen bonds : bond 0.03780 ( 379) hydrogen bonds : angle 4.77964 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7351 (ttp80) REVERT: A 17 LYS cc_start: 0.8115 (tppp) cc_final: 0.7866 (tppp) REVERT: A 29 ASP cc_start: 0.7815 (t70) cc_final: 0.7520 (t0) REVERT: A 44 ASP cc_start: 0.7335 (p0) cc_final: 0.6860 (p0) REVERT: A 62 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7710 (mtt90) REVERT: A 76 ARG cc_start: 0.7311 (ttt-90) cc_final: 0.7057 (ttt-90) REVERT: A 78 ASP cc_start: 0.7739 (m-30) cc_final: 0.7284 (m-30) REVERT: A 122 ASN cc_start: 0.8345 (t0) cc_final: 0.8106 (t0) REVERT: A 230 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8407 (ttpp) REVERT: A 250 LYS cc_start: 0.8314 (mttt) cc_final: 0.8085 (mptt) REVERT: H 28 SER cc_start: 0.8377 (t) cc_final: 0.8162 (m) REVERT: H 46 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7778 (mmpt) REVERT: H 111 ASP cc_start: 0.7773 (m-30) cc_final: 0.7555 (m-30) REVERT: R 233 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.5361 (ptp-170) REVERT: R 237 ILE cc_start: 0.7305 (tt) cc_final: 0.7102 (tt) REVERT: R 364 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7814 (mm-40) outliers start: 22 outliers final: 14 residues processed: 213 average time/residue: 0.5290 time to fit residues: 119.1550 Evaluate side-chains 207 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 364 GLN Chi-restraints excluded: chain R residue 445 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 HIS A 130 GLN A 153 ASN A 223 ASN A 299 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.142686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122142 restraints weight = 10285.788| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.32 r_work: 0.3493 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7291 Z= 0.206 Angle : 0.589 7.976 9901 Z= 0.309 Chirality : 0.044 0.175 1111 Planarity : 0.005 0.046 1230 Dihedral : 6.122 75.914 989 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.64 % Rotamer: Outliers : 2.99 % Allowed : 17.95 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.84 (0.29), residues: 863 helix: 1.80 (0.32), residues: 260 sheet: 0.24 (0.34), residues: 244 loop : -0.02 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 282 TYR 0.024 0.002 TYR R 191 PHE 0.025 0.002 PHE R 375 TRP 0.009 0.001 TRP R 352 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7288) covalent geometry : angle 0.58377 ( 9895) SS BOND : bond 0.00780 ( 3) SS BOND : angle 3.24883 ( 6) hydrogen bonds : bond 0.03875 ( 379) hydrogen bonds : angle 4.81530 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7373 (ttp80) REVERT: A 29 ASP cc_start: 0.7795 (t70) cc_final: 0.7498 (t0) REVERT: A 44 ASP cc_start: 0.7364 (p0) cc_final: 0.6800 (p0) REVERT: A 54 TYR cc_start: 0.7824 (m-10) cc_final: 0.7543 (m-10) REVERT: A 62 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7618 (mtt90) REVERT: A 103 ARG cc_start: 0.8407 (mtm180) cc_final: 0.8189 (mtm180) REVERT: A 122 ASN cc_start: 0.8337 (t0) cc_final: 0.8097 (t0) REVERT: A 149 PHE cc_start: 0.7887 (m-80) cc_final: 0.7452 (m-80) REVERT: A 250 LYS cc_start: 0.8331 (mttt) cc_final: 0.8107 (mptt) REVERT: A 270 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7756 (ttpt) REVERT: H 28 SER cc_start: 0.8376 (t) cc_final: 0.8169 (m) REVERT: H 46 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7873 (mmpt) REVERT: H 111 ASP cc_start: 0.7778 (m-30) cc_final: 0.7565 (m-30) REVERT: R 221 TYR cc_start: 0.8085 (m-80) cc_final: 0.7790 (m-80) REVERT: R 233 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.5408 (ptp-170) REVERT: R 310 ILE cc_start: 0.8804 (mt) cc_final: 0.8593 (mt) REVERT: R 312 MET cc_start: 0.7264 (mmm) cc_final: 0.7025 (mtp) REVERT: R 364 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7692 (mm-40) outliers start: 23 outliers final: 15 residues processed: 206 average time/residue: 0.5125 time to fit residues: 111.7545 Evaluate side-chains 218 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 364 GLN Chi-restraints excluded: chain R residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 21 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 153 ASN A 223 ASN A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.122911 restraints weight = 10334.472| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.34 r_work: 0.3503 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7291 Z= 0.176 Angle : 0.580 8.195 9901 Z= 0.302 Chirality : 0.043 0.155 1111 Planarity : 0.005 0.050 1230 Dihedral : 6.119 78.322 989 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 2.60 % Allowed : 19.38 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.86 (0.29), residues: 863 helix: 1.76 (0.32), residues: 263 sheet: 0.19 (0.33), residues: 248 loop : 0.07 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 282 TYR 0.024 0.001 TYR R 191 PHE 0.029 0.002 PHE R 375 TRP 0.010 0.001 TRP R 352 HIS 0.004 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7288) covalent geometry : angle 0.57615 ( 9895) SS BOND : bond 0.00609 ( 3) SS BOND : angle 2.63014 ( 6) hydrogen bonds : bond 0.03767 ( 379) hydrogen bonds : angle 4.76147 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7361 (ttp80) REVERT: A 29 ASP cc_start: 0.7808 (t70) cc_final: 0.7523 (t0) REVERT: A 52 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7974 (ptp-110) REVERT: A 62 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7600 (mtt90) REVERT: A 76 ARG cc_start: 0.7321 (ttt-90) cc_final: 0.7015 (ttt-90) REVERT: A 81 VAL cc_start: 0.8682 (m) cc_final: 0.8444 (t) REVERT: A 103 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8199 (mtm180) REVERT: A 122 ASN cc_start: 0.8328 (t0) cc_final: 0.8097 (t0) REVERT: A 250 LYS cc_start: 0.8324 (mttt) cc_final: 0.8102 (mptt) REVERT: A 270 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7826 (ttpt) REVERT: H 46 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7913 (mmpt) REVERT: R 221 TYR cc_start: 0.8218 (m-80) cc_final: 0.7945 (m-80) REVERT: R 233 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.5356 (ptp-170) REVERT: R 310 ILE cc_start: 0.8803 (mt) cc_final: 0.8593 (mt) REVERT: R 312 MET cc_start: 0.7209 (mmm) cc_final: 0.6976 (mtp) outliers start: 20 outliers final: 13 residues processed: 213 average time/residue: 0.5113 time to fit residues: 115.3357 Evaluate side-chains 212 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 130 GLN A 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122731 restraints weight = 10312.577| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.34 r_work: 0.3498 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7291 Z= 0.183 Angle : 0.610 13.697 9901 Z= 0.317 Chirality : 0.044 0.186 1111 Planarity : 0.005 0.053 1230 Dihedral : 6.133 80.032 989 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 2.34 % Allowed : 20.16 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.77 (0.29), residues: 863 helix: 1.71 (0.32), residues: 263 sheet: 0.12 (0.33), residues: 244 loop : 0.01 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 282 TYR 0.033 0.002 TYR R 191 PHE 0.039 0.002 PHE R 375 TRP 0.016 0.002 TRP R 352 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7288) covalent geometry : angle 0.60040 ( 9895) SS BOND : bond 0.00622 ( 3) SS BOND : angle 4.44712 ( 6) hydrogen bonds : bond 0.03864 ( 379) hydrogen bonds : angle 4.77430 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7359 (ttp80) REVERT: A 29 ASP cc_start: 0.7808 (t70) cc_final: 0.7517 (t0) REVERT: A 62 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7640 (mtt90) REVERT: A 76 ARG cc_start: 0.7292 (ttt-90) cc_final: 0.6974 (ttt-90) REVERT: A 77 LYS cc_start: 0.8319 (tttt) cc_final: 0.8110 (tttt) REVERT: A 81 VAL cc_start: 0.8699 (m) cc_final: 0.8477 (t) REVERT: A 103 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8204 (mtm180) REVERT: A 122 ASN cc_start: 0.8313 (t0) cc_final: 0.8086 (t0) REVERT: A 270 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7807 (ttpt) REVERT: H 46 LYS cc_start: 0.8179 (mmpt) cc_final: 0.7927 (mmpt) REVERT: H 63 TYR cc_start: 0.8559 (m-80) cc_final: 0.8305 (m-80) REVERT: R 221 TYR cc_start: 0.8199 (m-80) cc_final: 0.7979 (m-80) REVERT: R 233 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.5333 (ptp-170) REVERT: R 282 ARG cc_start: 0.7147 (mmt-90) cc_final: 0.6777 (mpt90) outliers start: 18 outliers final: 15 residues processed: 206 average time/residue: 0.5349 time to fit residues: 116.4787 Evaluate side-chains 208 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 130 GLN A 153 ASN A 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.143189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122244 restraints weight = 10294.027| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.41 r_work: 0.3485 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7291 Z= 0.208 Angle : 0.630 13.559 9901 Z= 0.327 Chirality : 0.045 0.260 1111 Planarity : 0.005 0.054 1230 Dihedral : 6.246 82.477 989 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.64 % Rotamer: Outliers : 2.34 % Allowed : 20.42 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.76 (0.29), residues: 863 helix: 1.66 (0.32), residues: 263 sheet: 0.13 (0.33), residues: 248 loop : 0.04 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 282 TYR 0.028 0.002 TYR R 191 PHE 0.052 0.002 PHE R 375 TRP 0.016 0.002 TRP R 352 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 7288) covalent geometry : angle 0.62014 ( 9895) SS BOND : bond 0.00819 ( 3) SS BOND : angle 4.62519 ( 6) hydrogen bonds : bond 0.03938 ( 379) hydrogen bonds : angle 4.84175 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: P 19 ARG cc_start: 0.7310 (ttp80) cc_final: 0.7088 (ttp80) REVERT: A 29 ASP cc_start: 0.7629 (t70) cc_final: 0.7344 (t0) REVERT: A 62 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7323 (mtt90) REVERT: A 76 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.6581 (ttt-90) REVERT: A 77 LYS cc_start: 0.8188 (tttt) cc_final: 0.7903 (mtpm) REVERT: A 81 VAL cc_start: 0.8611 (m) cc_final: 0.8386 (t) REVERT: A 122 ASN cc_start: 0.8182 (t0) cc_final: 0.7915 (t0) REVERT: A 249 TYR cc_start: 0.7895 (m-80) cc_final: 0.7652 (m-80) REVERT: A 270 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7642 (ttpt) REVERT: H 46 LYS cc_start: 0.8048 (mmpt) cc_final: 0.7833 (mmpt) REVERT: H 63 TYR cc_start: 0.8467 (m-80) cc_final: 0.8217 (m-80) REVERT: R 233 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.5192 (ptp-170) REVERT: R 282 ARG cc_start: 0.7209 (mmt-90) cc_final: 0.6869 (mpt90) outliers start: 18 outliers final: 15 residues processed: 201 average time/residue: 0.5171 time to fit residues: 110.1413 Evaluate side-chains 212 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121625 restraints weight = 10235.083| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.40 r_work: 0.3477 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7291 Z= 0.232 Angle : 0.648 13.446 9901 Z= 0.337 Chirality : 0.046 0.231 1111 Planarity : 0.005 0.053 1230 Dihedral : 6.322 83.112 989 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 2.34 % Allowed : 21.07 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.12 % 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: 0.67 (0.29), residues: 863 helix: 1.59 (0.32), residues: 263 sheet: 0.09 (0.33), residues: 244 loop : -0.04 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 282 TYR 0.036 0.002 TYR R 191 PHE 0.059 0.002 PHE R 375 TRP 0.015 0.002 TRP R 352 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 7288) covalent geometry : angle 0.63790 ( 9895) SS BOND : bond 0.00875 ( 3) SS BOND : angle 4.57182 ( 6) hydrogen bonds : bond 0.04008 ( 379) hydrogen bonds : angle 4.89385 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.77 seconds wall clock time: 50 minutes 56.37 seconds (3056.37 seconds total)