Starting phenix.real_space_refine on Sun Apr 5 02:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lz1_63518/04_2026/9lz1_63518.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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 2 5.49 5 S 30 5.16 5 C 4558 2.51 5 N 1192 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 7059 Number of models: 1 Model: "" Number of chains: 5 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: "P" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2273 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 272} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 7 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 Time building chain proxies: 1.66, per 1000 atoms: 0.24 Number of scatterers: 7059 At special positions: 0 Unit cell: (75.33, 100.44, 156.24, 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 30 16.00 P 2 15.00 O 1277 8.00 N 1192 7.00 C 4558 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: 0.72 Conformation dependent library (CDL) restraints added in 201.2 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: 1672 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 32.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'P' and resid 2 through 32 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 311 Processing helix chain 'R' and resid 316 through 347 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: 3.776A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) 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 sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, 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=AA3, 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: 7.879A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.585A 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) Processing sheet with id=AA6, first strand: chain 'R' and resid 504 through 505 removed outlier: 3.641A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 6.812A 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: 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: 6.684A 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=AA8, 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: 6.812A 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=AA9, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AB1, 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: 7.252A 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=AB2, 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: 7.252A 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) 405 hydrogen bonds defined for protein. 1119 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: 0.91 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: 1106 1.31 - 1.44: 2051 1.44 - 1.57: 4026 1.57 - 1.70: 3 1.70 - 1.82: 44 Bond restraints: 7230 Sorted by residual: bond pdb=" OG1 TPO R 503 " pdb=" P TPO R 503 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" O2P SEP R 504 " pdb=" P SEP R 504 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O1P SEP R 504 " pdb=" P SEP R 504 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3P SEP R 504 " pdb=" P SEP R 504 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CA ALA R 313 " pdb=" C ALA R 313 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.13e+01 ... (remaining 7225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 9684 2.74 - 5.49: 104 5.49 - 8.23: 15 8.23 - 10.98: 5 10.98 - 13.72: 5 Bond angle restraints: 9813 Sorted by residual: angle pdb=" N PHE R 314 " pdb=" CA PHE R 314 " pdb=" C PHE R 314 " ideal model delta sigma weight residual 111.30 99.80 11.50 1.36e+00 5.41e-01 7.15e+01 angle pdb=" N MET R 312 " pdb=" CA MET R 312 " pdb=" C MET R 312 " ideal model delta sigma weight residual 109.86 97.68 12.18 1.55e+00 4.16e-01 6.18e+01 angle pdb=" CA TPO R 503 " pdb=" C TPO R 503 " pdb=" N SEP R 504 " ideal model delta sigma weight residual 116.20 102.48 13.72 2.00e+00 2.50e-01 4.71e+01 angle pdb=" CA PRO A 120 " pdb=" N PRO A 120 " pdb=" CD PRO A 120 " ideal model delta sigma weight residual 112.00 103.27 8.73 1.40e+00 5.10e-01 3.89e+01 angle pdb=" CA TPO R 503 " pdb=" C TPO R 503 " pdb=" O TPO R 503 " ideal model delta sigma weight residual 120.80 130.89 -10.09 1.70e+00 3.46e-01 3.52e+01 ... (remaining 9808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3996 17.83 - 35.65: 233 35.65 - 53.47: 48 53.47 - 71.30: 14 71.30 - 89.12: 3 Dihedral angle restraints: 4294 sinusoidal: 1700 harmonic: 2594 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 180.00 150.78 29.22 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 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 4291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 731 0.038 - 0.076: 261 0.076 - 0.113: 82 0.113 - 0.151: 24 0.151 - 0.189: 8 Chirality restraints: 1106 Sorted by residual: 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 8.90e-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 8.05e-01 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1103 not shown) Planarity restraints: 1223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TPO R 503 " -0.059 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" C TPO R 503 " 0.191 2.00e-02 2.50e+03 pdb=" O TPO R 503 " -0.082 2.00e-02 2.50e+03 pdb=" N SEP R 504 " -0.051 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 1.73e+01 pdb=" N PRO A 120 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.051 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 9.22e-02 1.36e+01 pdb=" N PRO A 131 " 0.159 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 1220 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 67 2.56 - 3.14: 5528 3.14 - 3.73: 10936 3.73 - 4.31: 15311 4.31 - 4.90: 25877 Nonbonded interactions: 57719 Sorted by model distance: nonbonded pdb=" O VAL R 412 " pdb=" OH TYR R 459 " model vdw 1.969 3.040 nonbonded pdb=" OG SER L 32 " pdb=" NH1 ARG A 7 " model vdw 2.031 3.120 nonbonded pdb=" OD2 ASP A 260 " pdb=" OH TYR A 272 " model vdw 2.178 3.040 nonbonded pdb=" O PHE R 311 " pdb=" CD1 PHE A 244 " model vdw 2.188 3.340 nonbonded pdb=" OD1 ASP A 204 " pdb=" OH TYR A 208 " model vdw 2.197 3.040 ... (remaining 57714 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: 2.110 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 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 0.106 7233 Z= 0.323 Angle : 0.798 13.719 9819 Z= 0.447 Chirality : 0.046 0.189 1106 Planarity : 0.007 0.111 1223 Dihedral : 12.519 89.124 2613 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.71 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % 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: 0.67 (0.30), residues: 863 helix: 1.72 (0.33), residues: 262 sheet: 0.10 (0.36), residues: 234 loop : -0.16 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 282 TYR 0.031 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 0.00590 ( 7230) covalent geometry : angle 0.79406 ( 9813) SS BOND : bond 0.00556 ( 3) SS BOND : angle 3.29660 ( 6) hydrogen bonds : bond 0.16497 ( 374) hydrogen bonds : angle 7.63438 ( 1119) *********************** 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 303 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6513 (mtp) cc_final: 0.6246 (mtp) REVERT: A 207 ILE cc_start: 0.8001 (mm) cc_final: 0.7710 (mt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.0990 time to fit residues: 38.3159 Evaluate side-chains 193 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN L 7 GLN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.223371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154322 restraints weight = 8503.408| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.38 r_work: 0.3736 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7233 Z= 0.198 Angle : 0.724 9.484 9819 Z= 0.378 Chirality : 0.046 0.185 1106 Planarity : 0.006 0.055 1223 Dihedral : 5.585 65.280 973 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.78 % Allowed : 13.54 % Favored : 82.68 % 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: 0.63 (0.29), residues: 863 helix: 1.47 (0.32), residues: 261 sheet: 0.27 (0.34), residues: 242 loop : -0.14 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 76 TYR 0.054 0.003 TYR R 191 PHE 0.019 0.003 PHE R 287 TRP 0.019 0.002 TRP P 14 HIS 0.007 0.002 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7230) covalent geometry : angle 0.72103 ( 9813) SS BOND : bond 0.00906 ( 3) SS BOND : angle 2.56743 ( 6) hydrogen bonds : bond 0.04328 ( 374) hydrogen bonds : angle 5.16336 ( 1119) *********************** 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 243 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 8 MET cc_start: 0.9412 (mmm) cc_final: 0.9155 (tpp) REVERT: R 375 PHE cc_start: 0.6933 (m-10) cc_final: 0.6467 (m-10) REVERT: R 413 LEU cc_start: 0.9032 (tp) cc_final: 0.8809 (tp) REVERT: R 429 TYR cc_start: 0.6112 (m-10) cc_final: 0.5713 (m-80) REVERT: A 10 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7338 (ptmt) REVERT: A 153 ASN cc_start: 0.7374 (t0) cc_final: 0.7128 (t0) REVERT: A 207 ILE cc_start: 0.8619 (mm) cc_final: 0.8275 (mt) REVERT: A 248 GLN cc_start: 0.8022 (tt0) cc_final: 0.7753 (tt0) outliers start: 29 outliers final: 21 residues processed: 229 average time/residue: 0.0914 time to fit residues: 27.2062 Evaluate side-chains 190 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 301 VAL Chi-restraints excluded: chain R residue 432 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 325 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 393 ASN ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.217674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143256 restraints weight = 8449.006| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.79 r_work: 0.3583 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7233 Z= 0.225 Angle : 0.699 7.843 9819 Z= 0.364 Chirality : 0.047 0.209 1106 Planarity : 0.005 0.054 1223 Dihedral : 5.512 64.129 973 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.43 % Allowed : 18.62 % Favored : 76.95 % 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: 0.49 (0.29), residues: 863 helix: 1.44 (0.32), residues: 257 sheet: 0.08 (0.33), residues: 253 loop : -0.21 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 213 TYR 0.041 0.003 TYR R 191 PHE 0.025 0.002 PHE A 117 TRP 0.019 0.002 TRP P 14 HIS 0.007 0.002 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 7230) covalent geometry : angle 0.69839 ( 9813) SS BOND : bond 0.00940 ( 3) SS BOND : angle 1.69010 ( 6) hydrogen bonds : bond 0.04102 ( 374) hydrogen bonds : angle 5.16808 ( 1119) *********************** 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 214 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 107 ILE cc_start: 0.6605 (mt) cc_final: 0.6387 (pt) REVERT: P 19 ARG cc_start: 0.5804 (tmt170) cc_final: 0.5531 (tmm160) REVERT: R 195 TYR cc_start: 0.7290 (m-80) cc_final: 0.7023 (m-80) REVERT: A 207 ILE cc_start: 0.8986 (mm) cc_final: 0.8686 (mt) REVERT: A 248 GLN cc_start: 0.8190 (tt0) cc_final: 0.7961 (tt0) outliers start: 34 outliers final: 26 residues processed: 199 average time/residue: 0.1003 time to fit residues: 25.4893 Evaluate side-chains 189 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 198 SER Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 442 HIS ** R 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.218827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146855 restraints weight = 8560.662| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.71 r_work: 0.3582 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7233 Z= 0.154 Angle : 0.656 10.310 9819 Z= 0.340 Chirality : 0.044 0.165 1106 Planarity : 0.005 0.049 1223 Dihedral : 5.272 59.384 973 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.69 % Allowed : 17.45 % Favored : 77.86 % 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: 0.45 (0.29), residues: 863 helix: 1.40 (0.33), residues: 259 sheet: -0.05 (0.32), residues: 264 loop : -0.13 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 51 TYR 0.044 0.002 TYR R 191 PHE 0.032 0.002 PHE R 291 TRP 0.016 0.002 TRP P 14 HIS 0.011 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7230) covalent geometry : angle 0.65144 ( 9813) SS BOND : bond 0.00590 ( 3) SS BOND : angle 3.34369 ( 6) hydrogen bonds : bond 0.03943 ( 374) hydrogen bonds : angle 4.94315 ( 1119) *********************** 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 214 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 19 ARG cc_start: 0.5620 (tmt170) cc_final: 0.5285 (tmm160) REVERT: R 195 TYR cc_start: 0.7248 (m-80) cc_final: 0.7047 (m-80) REVERT: R 454 PHE cc_start: 0.8353 (m-10) cc_final: 0.8134 (m-10) REVERT: A 10 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7086 (ptmt) REVERT: A 160 LYS cc_start: 0.7530 (tppt) cc_final: 0.7105 (mtpp) REVERT: A 207 ILE cc_start: 0.9004 (mm) cc_final: 0.8757 (mt) outliers start: 36 outliers final: 28 residues processed: 194 average time/residue: 0.0960 time to fit residues: 24.0355 Evaluate side-chains 189 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 376 ILE Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN R 442 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.215276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137394 restraints weight = 8596.176| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.88 r_work: 0.3555 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7233 Z= 0.267 Angle : 0.750 12.236 9819 Z= 0.389 Chirality : 0.048 0.280 1106 Planarity : 0.005 0.048 1223 Dihedral : 5.668 56.396 973 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.34 % Allowed : 20.05 % Favored : 74.61 % 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: 0.18 (0.29), residues: 863 helix: 1.47 (0.32), residues: 257 sheet: -0.26 (0.32), residues: 259 loop : -0.49 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 213 TYR 0.042 0.003 TYR R 191 PHE 0.048 0.003 PHE R 291 TRP 0.018 0.003 TRP P 14 HIS 0.007 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 7230) covalent geometry : angle 0.74420 ( 9813) SS BOND : bond 0.00671 ( 3) SS BOND : angle 3.83296 ( 6) hydrogen bonds : bond 0.04138 ( 374) hydrogen bonds : angle 5.24614 ( 1119) *********************** 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 207 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 GLU cc_start: 0.7195 (pt0) cc_final: 0.6773 (pm20) REVERT: L 92 TYR cc_start: 0.7456 (m-10) cc_final: 0.6579 (m-10) REVERT: P 19 ARG cc_start: 0.5750 (tmt170) cc_final: 0.5447 (tmm160) REVERT: R 440 GLN cc_start: 0.8491 (tt0) cc_final: 0.7755 (tp-100) REVERT: A 153 ASN cc_start: 0.7798 (t0) cc_final: 0.7248 (t0) REVERT: A 160 LYS cc_start: 0.7711 (tppt) cc_final: 0.7224 (mtpp) REVERT: A 256 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7428 (tt0) outliers start: 41 outliers final: 29 residues processed: 187 average time/residue: 0.0880 time to fit residues: 21.5562 Evaluate side-chains 184 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 189 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 442 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.217279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140299 restraints weight = 8547.080| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.85 r_work: 0.3557 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7233 Z= 0.163 Angle : 0.680 14.196 9819 Z= 0.351 Chirality : 0.045 0.307 1106 Planarity : 0.004 0.048 1223 Dihedral : 5.272 57.011 973 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.43 % Allowed : 21.35 % Favored : 74.22 % 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: 0.16 (0.29), residues: 863 helix: 1.25 (0.32), residues: 261 sheet: -0.23 (0.32), residues: 259 loop : -0.38 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 233 TYR 0.047 0.002 TYR R 191 PHE 0.061 0.002 PHE R 291 TRP 0.012 0.002 TRP R 298 HIS 0.011 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7230) covalent geometry : angle 0.67515 ( 9813) SS BOND : bond 0.00395 ( 3) SS BOND : angle 3.35972 ( 6) hydrogen bonds : bond 0.03909 ( 374) hydrogen bonds : angle 4.97371 ( 1119) *********************** 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 201 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 GLU cc_start: 0.7228 (pt0) cc_final: 0.6842 (pm20) REVERT: L 92 TYR cc_start: 0.7532 (m-10) cc_final: 0.6548 (m-10) REVERT: L 101 GLN cc_start: 0.8210 (mm-40) cc_final: 0.8004 (mp10) REVERT: P 14 TRP cc_start: 0.8336 (t-100) cc_final: 0.7967 (t-100) REVERT: P 19 ARG cc_start: 0.5667 (tmt170) cc_final: 0.5384 (tmm160) REVERT: R 291 PHE cc_start: 0.8279 (m-80) cc_final: 0.7939 (m-80) REVERT: A 153 ASN cc_start: 0.7805 (t0) cc_final: 0.7243 (t0) REVERT: A 160 LYS cc_start: 0.7710 (tppt) cc_final: 0.7249 (mtpp) outliers start: 34 outliers final: 27 residues processed: 188 average time/residue: 0.0824 time to fit residues: 20.6756 Evaluate side-chains 182 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 442 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.213855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136601 restraints weight = 8454.956| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.80 r_work: 0.3537 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7233 Z= 0.198 Angle : 0.701 15.343 9819 Z= 0.362 Chirality : 0.046 0.319 1106 Planarity : 0.005 0.047 1223 Dihedral : 5.247 50.423 973 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.08 % Allowed : 21.88 % Favored : 73.05 % 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: 0.06 (0.28), residues: 863 helix: 1.16 (0.32), residues: 262 sheet: -0.31 (0.33), residues: 243 loop : -0.42 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 70 TYR 0.051 0.002 TYR R 191 PHE 0.048 0.002 PHE R 291 TRP 0.012 0.002 TRP R 361 HIS 0.011 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7230) covalent geometry : angle 0.69713 ( 9813) SS BOND : bond 0.00555 ( 3) SS BOND : angle 3.04738 ( 6) hydrogen bonds : bond 0.04007 ( 374) hydrogen bonds : angle 4.95855 ( 1119) *********************** 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 196 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 GLU cc_start: 0.7176 (pt0) cc_final: 0.6803 (pm20) REVERT: L 92 TYR cc_start: 0.7750 (m-10) cc_final: 0.6716 (m-80) REVERT: P 14 TRP cc_start: 0.8292 (t-100) cc_final: 0.7923 (t-100) REVERT: P 19 ARG cc_start: 0.5719 (tmt170) cc_final: 0.5435 (tmm160) REVERT: R 295 ASN cc_start: 0.7811 (t0) cc_final: 0.7568 (t0) REVERT: A 160 LYS cc_start: 0.7749 (tppt) cc_final: 0.7335 (mtpp) REVERT: A 256 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7458 (tt0) outliers start: 39 outliers final: 30 residues processed: 183 average time/residue: 0.0840 time to fit residues: 20.5716 Evaluate side-chains 179 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 442 HIS Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 442 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.215115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143423 restraints weight = 8561.503| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.81 r_work: 0.3519 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7233 Z= 0.153 Angle : 0.675 16.359 9819 Z= 0.348 Chirality : 0.045 0.329 1106 Planarity : 0.004 0.047 1223 Dihedral : 5.050 46.901 973 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.69 % Allowed : 22.79 % Favored : 72.53 % 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: 0.09 (0.29), residues: 863 helix: 1.21 (0.32), residues: 263 sheet: -0.32 (0.32), residues: 255 loop : -0.40 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 51 TYR 0.045 0.002 TYR R 191 PHE 0.057 0.002 PHE R 291 TRP 0.012 0.002 TRP R 437 HIS 0.022 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7230) covalent geometry : angle 0.67118 ( 9813) SS BOND : bond 0.00414 ( 3) SS BOND : angle 2.89976 ( 6) hydrogen bonds : bond 0.03793 ( 374) hydrogen bonds : angle 4.81604 ( 1119) *********************** 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 202 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.8525 (m-10) cc_final: 0.7700 (m-80) REVERT: H 115 GLN cc_start: 0.8258 (pt0) cc_final: 0.8041 (pt0) REVERT: L 82 GLU cc_start: 0.7316 (pt0) cc_final: 0.6944 (pm20) REVERT: L 92 TYR cc_start: 0.7759 (m-10) cc_final: 0.6733 (m-10) REVERT: P 19 ARG cc_start: 0.5712 (tmt170) cc_final: 0.5418 (tmm160) REVERT: R 191 TYR cc_start: 0.8918 (p90) cc_final: 0.8322 (p90) REVERT: R 295 ASN cc_start: 0.7842 (t0) cc_final: 0.7565 (t0) REVERT: R 440 GLN cc_start: 0.8442 (tt0) cc_final: 0.7675 (tp40) REVERT: A 160 LYS cc_start: 0.7751 (tppt) cc_final: 0.7348 (mtpp) REVERT: A 256 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7466 (tt0) outliers start: 36 outliers final: 29 residues processed: 187 average time/residue: 0.0852 time to fit residues: 21.0532 Evaluate side-chains 186 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 505 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 295 ASN R 442 HIS A 111 HIS A 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.215191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142083 restraints weight = 8483.927| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.61 r_work: 0.3515 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7233 Z= 0.168 Angle : 0.690 17.238 9819 Z= 0.356 Chirality : 0.045 0.339 1106 Planarity : 0.004 0.046 1223 Dihedral : 4.986 42.403 973 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.95 % Allowed : 23.18 % Favored : 71.88 % 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: 0.21 (0.29), residues: 863 helix: 1.38 (0.32), residues: 262 sheet: -0.23 (0.33), residues: 242 loop : -0.42 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.045 0.002 TYR R 191 PHE 0.053 0.002 PHE R 291 TRP 0.039 0.002 TRP P 14 HIS 0.012 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7230) covalent geometry : angle 0.68717 ( 9813) SS BOND : bond 0.00434 ( 3) SS BOND : angle 2.73578 ( 6) hydrogen bonds : bond 0.03794 ( 374) hydrogen bonds : angle 4.82234 ( 1119) *********************** 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 199 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.8548 (m-10) cc_final: 0.7549 (m-80) REVERT: L 82 GLU cc_start: 0.7268 (pt0) cc_final: 0.6876 (pm20) REVERT: L 92 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: P 19 ARG cc_start: 0.5592 (tmt170) cc_final: 0.5320 (tmm160) REVERT: R 191 TYR cc_start: 0.8823 (p90) cc_final: 0.8416 (p90) REVERT: R 291 PHE cc_start: 0.8292 (m-80) cc_final: 0.7957 (m-80) REVERT: R 440 GLN cc_start: 0.8434 (tt0) cc_final: 0.7627 (tp40) REVERT: A 160 LYS cc_start: 0.7822 (tppt) cc_final: 0.7425 (mtpp) REVERT: A 256 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7501 (tt0) outliers start: 38 outliers final: 31 residues processed: 183 average time/residue: 0.0961 time to fit residues: 22.9146 Evaluate side-chains 190 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain P residue 15 ILE Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 442 HIS A 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.214088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136832 restraints weight = 8512.831| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.80 r_work: 0.3547 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7233 Z= 0.172 Angle : 0.690 17.063 9819 Z= 0.358 Chirality : 0.045 0.336 1106 Planarity : 0.004 0.046 1223 Dihedral : 5.008 43.368 973 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.56 % Allowed : 24.22 % Favored : 71.22 % 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: 0.22 (0.29), residues: 863 helix: 1.45 (0.33), residues: 262 sheet: -0.34 (0.33), residues: 247 loop : -0.35 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.046 0.002 TYR R 191 PHE 0.047 0.002 PHE R 291 TRP 0.042 0.002 TRP P 14 HIS 0.013 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7230) covalent geometry : angle 0.68748 ( 9813) SS BOND : bond 0.00425 ( 3) SS BOND : angle 2.62092 ( 6) hydrogen bonds : bond 0.03782 ( 374) hydrogen bonds : angle 4.81273 ( 1119) ********************** 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 198 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 58 TYR cc_start: 0.8498 (m-10) cc_final: 0.7586 (m-80) REVERT: L 49 ILE cc_start: 0.8382 (mt) cc_final: 0.8177 (mt) REVERT: L 82 GLU cc_start: 0.7226 (pt0) cc_final: 0.6920 (pm20) REVERT: L 92 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6812 (m-10) REVERT: L 106 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: P 19 ARG cc_start: 0.5697 (tmt170) cc_final: 0.5428 (tmm160) REVERT: R 191 TYR cc_start: 0.8812 (p90) cc_final: 0.8504 (p90) REVERT: R 225 HIS cc_start: 0.8181 (m170) cc_final: 0.7943 (t-90) REVERT: R 291 PHE cc_start: 0.8284 (m-80) cc_final: 0.7972 (m-80) REVERT: R 440 GLN cc_start: 0.8421 (tt0) cc_final: 0.7615 (tp40) REVERT: A 49 LYS cc_start: 0.8667 (pttm) cc_final: 0.8453 (mtmm) REVERT: A 160 LYS cc_start: 0.7830 (tppt) cc_final: 0.7427 (mtpp) REVERT: A 256 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7580 (tt0) outliers start: 35 outliers final: 30 residues processed: 185 average time/residue: 0.0816 time to fit residues: 20.1516 Evaluate side-chains 193 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 442 HIS Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 442 HIS A 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.214311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140401 restraints weight = 8528.056| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.58 r_work: 0.3516 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7233 Z= 0.155 Angle : 0.696 17.397 9819 Z= 0.360 Chirality : 0.045 0.334 1106 Planarity : 0.005 0.046 1223 Dihedral : 4.915 43.925 973 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.43 % Allowed : 25.26 % Favored : 70.31 % 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: 0.19 (0.29), residues: 863 helix: 1.29 (0.32), residues: 262 sheet: -0.27 (0.33), residues: 247 loop : -0.33 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 307 TYR 0.046 0.002 TYR R 191 PHE 0.046 0.002 PHE R 291 TRP 0.043 0.002 TRP P 14 HIS 0.014 0.002 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7230) covalent geometry : angle 0.69301 ( 9813) SS BOND : bond 0.00383 ( 3) SS BOND : angle 2.55355 ( 6) hydrogen bonds : bond 0.03778 ( 374) hydrogen bonds : angle 4.81101 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.02 seconds wall clock time: 39 minutes 16.52 seconds (2356.52 seconds total)