Starting phenix.real_space_refine on Tue Mar 3 13:06:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806.map" model { file = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ukj_20806/03_2026/6ukj_20806_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3037 2.51 5 N 723 2.21 5 O 837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4625 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2810 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 986 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.26, per 1000 atoms: 0.27 Number of scatterers: 4625 At special positions: 0 Unit cell: (63.135, 84.87, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 837 8.00 N 723 7.00 C 3037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 312 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 309 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 48.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.232A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.858A pdb=" N MET A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 Processing helix chain 'A' and resid 126 through 148 Processing helix chain 'A' and resid 152 through 174 removed outlier: 3.949A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 180 through 205 removed outlier: 3.915A pdb=" N GLU A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.598A pdb=" N TYR A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 314 through 340 removed outlier: 4.388A pdb=" N THR A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.753A pdb=" N ILE A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 removed outlier: 3.622A pdb=" N ALA A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 404 removed outlier: 3.692A pdb=" N PHE A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.502A pdb=" N TYR H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 35' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.804A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.622A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP H 76 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.904A pdb=" N CYS H 99 " --> pdb=" O TRP H 122 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP H 122 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG H 101 " --> pdb=" O ASP H 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 50 Processing sheet with id=AA4, first strand: chain 'H' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.535A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.550A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 786 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: 0.82 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 711 1.32 - 1.44: 1397 1.44 - 1.57: 2590 1.57 - 1.69: 1 1.69 - 1.81: 41 Bond restraints: 4740 Sorted by residual: bond pdb=" C PRO L 9 " pdb=" O PRO L 9 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 8.98e+00 bond pdb=" CA SER L 10 " pdb=" CB SER L 10 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.55e-02 4.16e+03 6.64e+00 bond pdb=" N GLN L 7 " pdb=" CA GLN L 7 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N SER L 8 " pdb=" CA SER L 8 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.41e-02 5.03e+03 6.07e+00 bond pdb=" CA SER L 11 " pdb=" CB SER L 11 " ideal model delta sigma weight residual 1.534 1.492 0.042 1.72e-02 3.38e+03 5.85e+00 ... (remaining 4735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 6170 1.92 - 3.85: 222 3.85 - 5.77: 33 5.77 - 7.70: 11 7.70 - 9.62: 4 Bond angle restraints: 6440 Sorted by residual: angle pdb=" N PRO L 9 " pdb=" CA PRO L 9 " pdb=" C PRO L 9 " ideal model delta sigma weight residual 112.47 104.55 7.92 2.06e+00 2.36e-01 1.48e+01 angle pdb=" C GLN L 7 " pdb=" N SER L 8 " pdb=" CA SER L 8 " ideal model delta sigma weight residual 121.80 130.34 -8.54 2.44e+00 1.68e-01 1.22e+01 angle pdb=" O GLN L 7 " pdb=" C GLN L 7 " pdb=" N SER L 8 " ideal model delta sigma weight residual 123.22 126.77 -3.55 1.14e+00 7.69e-01 9.70e+00 angle pdb=" CB GLN L 7 " pdb=" CG GLN L 7 " pdb=" CD GLN L 7 " ideal model delta sigma weight residual 112.60 107.55 5.05 1.70e+00 3.46e-01 8.84e+00 angle pdb=" C ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta sigma weight residual 112.26 107.55 4.71 1.62e+00 3.81e-01 8.45e+00 ... (remaining 6435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 2502 16.66 - 33.33: 244 33.33 - 49.99: 56 49.99 - 66.65: 8 66.65 - 83.31: 2 Dihedral angle restraints: 2812 sinusoidal: 1106 harmonic: 1706 Sorted by residual: dihedral pdb=" CB CYS A 301 " pdb=" SG CYS A 301 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual -86.00 -154.46 68.46 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 44.16 48.84 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA LEU A 175 " pdb=" C LEU A 175 " pdb=" N ARG A 176 " pdb=" CA ARG A 176 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 654 0.076 - 0.152: 78 0.152 - 0.228: 4 0.228 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 739 Sorted by residual: chirality pdb=" CBG Y01 A 501 " pdb=" CAQ Y01 A 501 " pdb=" CBD Y01 A 501 " pdb=" CBI Y01 A 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CBF Y01 A 501 " pdb=" CAS Y01 A 501 " pdb=" CBD Y01 A 501 " pdb=" CBH Y01 A 501 " both_signs ideal model delta sigma weight residual False -2.45 -2.71 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO L 9 " pdb=" N PRO L 9 " pdb=" C PRO L 9 " pdb=" CB PRO L 9 " both_signs ideal model delta sigma weight residual False 2.72 2.97 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 736 not shown) Planarity restraints: 788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 8 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C SER L 8 " 0.041 2.00e-02 2.50e+03 pdb=" O SER L 8 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO L 9 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 95 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO L 96 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER L 11 " 0.008 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C SER L 11 " -0.030 2.00e-02 2.50e+03 pdb=" O SER L 11 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU L 12 " 0.010 2.00e-02 2.50e+03 ... (remaining 785 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 86 2.67 - 3.23: 4571 3.23 - 3.79: 7169 3.79 - 4.34: 9760 4.34 - 4.90: 16423 Nonbonded interactions: 38009 Sorted by model distance: nonbonded pdb=" O ILE A 347 " pdb=" OH TYR A 384 " model vdw 2.114 3.040 nonbonded pdb=" OG SER A 72 " pdb=" OE1 GLN A 352 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 157 " pdb=" OE2 GLU A 198 " model vdw 2.260 3.040 nonbonded pdb=" OG SER L 8 " pdb=" CD PRO L 9 " model vdw 2.262 3.440 nonbonded pdb=" OE2 GLU A 208 " pdb=" NZ LYS A 270 " model vdw 2.284 3.120 ... (remaining 38004 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: 2.700 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 4745 Z= 0.323 Angle : 0.908 9.621 6448 Z= 0.477 Chirality : 0.052 0.381 739 Planarity : 0.005 0.047 788 Dihedral : 13.739 83.312 1708 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.28), residues: 574 helix: -1.69 (0.25), residues: 263 sheet: -1.94 (0.47), residues: 93 loop : -2.58 (0.34), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 231 TYR 0.019 0.002 TYR H 102 PHE 0.018 0.002 PHE A 251 TRP 0.013 0.002 TRP L 95 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00712 ( 4740) covalent geometry : angle 0.90716 ( 6440) SS BOND : bond 0.00839 ( 4) SS BOND : angle 1.62881 ( 8) hydrogen bonds : bond 0.10853 ( 263) hydrogen bonds : angle 5.64310 ( 786) Misc. bond : bond 0.03126 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8051 (ptpt) REVERT: A 218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8237 (mp) REVERT: A 307 LYS cc_start: 0.8745 (mptt) cc_final: 0.8526 (mmtt) REVERT: A 347 ILE cc_start: 0.8027 (mm) cc_final: 0.7775 (mt) REVERT: A 384 TYR cc_start: 0.8336 (t80) cc_final: 0.7693 (t80) REVERT: A 397 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6664 (mp) REVERT: H 68 LYS cc_start: 0.8338 (tttt) cc_final: 0.7973 (ttpp) REVERT: H 80 ASN cc_start: 0.8448 (t0) cc_final: 0.8204 (t0) REVERT: L 56 TYR cc_start: 0.8449 (t80) cc_final: 0.8003 (t80) outliers start: 4 outliers final: 2 residues processed: 129 average time/residue: 0.0925 time to fit residues: 14.2165 Evaluate side-chains 103 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain L residue 10 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111337 restraints weight = 7765.688| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.94 r_work: 0.3248 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4745 Z= 0.170 Angle : 0.616 7.573 6448 Z= 0.324 Chirality : 0.043 0.180 739 Planarity : 0.004 0.043 788 Dihedral : 7.836 55.978 710 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.17 % Allowed : 11.31 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.32), residues: 574 helix: -0.16 (0.30), residues: 266 sheet: -1.19 (0.51), residues: 91 loop : -2.18 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 41 TYR 0.014 0.001 TYR A 345 PHE 0.015 0.001 PHE A 268 TRP 0.014 0.001 TRP L 95 HIS 0.003 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 4740) covalent geometry : angle 0.61466 ( 6440) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.25989 ( 8) hydrogen bonds : bond 0.05141 ( 263) hydrogen bonds : angle 4.71942 ( 786) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7858 (t80) REVERT: A 106 PHE cc_start: 0.7939 (t80) cc_final: 0.6991 (m-10) REVERT: A 310 ASP cc_start: 0.8771 (p0) cc_final: 0.8514 (p0) REVERT: A 333 THR cc_start: 0.9015 (m) cc_final: 0.8780 (m) REVERT: A 347 ILE cc_start: 0.8731 (mm) cc_final: 0.8331 (mt) REVERT: A 384 TYR cc_start: 0.8955 (t80) cc_final: 0.8555 (t80) REVERT: H 68 LYS cc_start: 0.8467 (tttt) cc_final: 0.8039 (ttpp) REVERT: H 80 ASN cc_start: 0.8569 (t0) cc_final: 0.8255 (t0) REVERT: L 56 TYR cc_start: 0.8901 (t80) cc_final: 0.8591 (t80) REVERT: L 91 GLN cc_start: 0.9129 (pp30) cc_final: 0.8190 (pp30) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 0.0719 time to fit residues: 11.8682 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 214 ASN H 38 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113662 restraints weight = 7759.567| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.93 r_work: 0.3286 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4745 Z= 0.145 Angle : 0.574 7.465 6448 Z= 0.301 Chirality : 0.042 0.157 739 Planarity : 0.004 0.041 788 Dihedral : 7.066 59.813 705 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.37 % Allowed : 15.08 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.34), residues: 574 helix: 0.54 (0.31), residues: 269 sheet: -0.77 (0.54), residues: 91 loop : -1.82 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 111 TYR 0.012 0.001 TYR A 345 PHE 0.014 0.001 PHE A 251 TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4740) covalent geometry : angle 0.57326 ( 6440) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.09011 ( 8) hydrogen bonds : bond 0.04894 ( 263) hydrogen bonds : angle 4.51438 ( 786) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7832 (t80) cc_final: 0.6898 (m-10) REVERT: A 299 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 305 MET cc_start: 0.8730 (mtp) cc_final: 0.8411 (mmm) REVERT: A 310 ASP cc_start: 0.8655 (p0) cc_final: 0.8426 (p0) REVERT: A 325 PHE cc_start: 0.9141 (m-10) cc_final: 0.8887 (m-80) REVERT: A 333 THR cc_start: 0.9096 (m) cc_final: 0.8798 (m) REVERT: A 347 ILE cc_start: 0.8751 (mm) cc_final: 0.8396 (mt) REVERT: A 384 TYR cc_start: 0.8945 (t80) cc_final: 0.8541 (t80) REVERT: H 68 LYS cc_start: 0.8454 (tttt) cc_final: 0.8057 (ttpp) REVERT: H 80 ASN cc_start: 0.8618 (t0) cc_final: 0.8306 (t0) REVERT: L 56 TYR cc_start: 0.8920 (t80) cc_final: 0.8688 (t80) REVERT: L 91 GLN cc_start: 0.9186 (pp30) cc_final: 0.8239 (pp30) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.0703 time to fit residues: 11.2298 Evaluate side-chains 122 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114444 restraints weight = 7782.933| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.94 r_work: 0.3296 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4745 Z= 0.128 Angle : 0.581 10.883 6448 Z= 0.297 Chirality : 0.041 0.142 739 Planarity : 0.004 0.042 788 Dihedral : 6.926 59.477 705 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.37 % Allowed : 16.27 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.35), residues: 574 helix: 0.93 (0.31), residues: 269 sheet: -0.70 (0.56), residues: 91 loop : -1.61 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.012 0.001 TYR A 345 PHE 0.023 0.001 PHE A 268 TRP 0.010 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4740) covalent geometry : angle 0.58059 ( 6440) SS BOND : bond 0.00362 ( 4) SS BOND : angle 1.00686 ( 8) hydrogen bonds : bond 0.04724 ( 263) hydrogen bonds : angle 4.45526 ( 786) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.9137 (m-10) cc_final: 0.8916 (m-80) REVERT: A 333 THR cc_start: 0.9102 (m) cc_final: 0.8794 (m) REVERT: A 347 ILE cc_start: 0.8734 (mm) cc_final: 0.8387 (mt) REVERT: A 384 TYR cc_start: 0.8986 (t80) cc_final: 0.8664 (t80) REVERT: H 49 GLU cc_start: 0.8401 (tt0) cc_final: 0.8148 (tt0) REVERT: H 68 LYS cc_start: 0.8406 (tttt) cc_final: 0.8022 (ttpp) REVERT: H 80 ASN cc_start: 0.8524 (t0) cc_final: 0.8224 (t0) REVERT: H 102 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8394 (m-10) REVERT: L 56 TYR cc_start: 0.8939 (t80) cc_final: 0.8645 (t80) REVERT: L 91 GLN cc_start: 0.9209 (pp30) cc_final: 0.8149 (pp30) outliers start: 22 outliers final: 19 residues processed: 131 average time/residue: 0.0666 time to fit residues: 10.9124 Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 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 214 ASN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113347 restraints weight = 7804.318| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.95 r_work: 0.3282 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4745 Z= 0.141 Angle : 0.581 8.554 6448 Z= 0.300 Chirality : 0.042 0.148 739 Planarity : 0.004 0.041 788 Dihedral : 6.854 58.649 705 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.96 % Allowed : 17.06 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.35), residues: 574 helix: 1.13 (0.32), residues: 270 sheet: -0.54 (0.57), residues: 90 loop : -1.54 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 111 TYR 0.013 0.001 TYR A 345 PHE 0.017 0.001 PHE A 268 TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4740) covalent geometry : angle 0.57992 ( 6440) SS BOND : bond 0.00350 ( 4) SS BOND : angle 1.03163 ( 8) hydrogen bonds : bond 0.04835 ( 263) hydrogen bonds : angle 4.43928 ( 786) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 PHE cc_start: 0.9123 (m-10) cc_final: 0.8920 (m-80) REVERT: A 333 THR cc_start: 0.9125 (m) cc_final: 0.8819 (m) REVERT: A 347 ILE cc_start: 0.8723 (mm) cc_final: 0.8429 (mt) REVERT: A 384 TYR cc_start: 0.8980 (t80) cc_final: 0.8603 (t80) REVERT: H 49 GLU cc_start: 0.8393 (tt0) cc_final: 0.8134 (tt0) REVERT: H 68 LYS cc_start: 0.8405 (tttt) cc_final: 0.7998 (ttpp) REVERT: H 80 ASN cc_start: 0.8495 (t0) cc_final: 0.8204 (t0) REVERT: L 18 ASP cc_start: 0.8122 (m-30) cc_final: 0.7908 (m-30) REVERT: L 56 TYR cc_start: 0.8961 (t80) cc_final: 0.8595 (t80) REVERT: L 91 GLN cc_start: 0.9249 (pp30) cc_final: 0.8317 (pp30) outliers start: 25 outliers final: 21 residues processed: 129 average time/residue: 0.0667 time to fit residues: 10.8701 Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116235 restraints weight = 7923.951| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3324 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4745 Z= 0.116 Angle : 0.558 8.365 6448 Z= 0.285 Chirality : 0.041 0.129 739 Planarity : 0.004 0.042 788 Dihedral : 6.636 59.447 705 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.16 % Allowed : 18.06 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.35), residues: 574 helix: 1.30 (0.31), residues: 272 sheet: -0.44 (0.57), residues: 90 loop : -1.43 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 111 TYR 0.009 0.001 TYR A 345 PHE 0.017 0.001 PHE A 268 TRP 0.007 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4740) covalent geometry : angle 0.55747 ( 6440) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.97292 ( 8) hydrogen bonds : bond 0.04484 ( 263) hydrogen bonds : angle 4.32321 ( 786) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7744 (t80) cc_final: 0.6817 (m-80) REVERT: A 305 MET cc_start: 0.8618 (mtp) cc_final: 0.8305 (mmm) REVERT: A 333 THR cc_start: 0.9113 (m) cc_final: 0.8818 (m) REVERT: A 347 ILE cc_start: 0.8651 (mm) cc_final: 0.8358 (mt) REVERT: A 384 TYR cc_start: 0.8994 (t80) cc_final: 0.8675 (t80) REVERT: H 49 GLU cc_start: 0.8403 (tt0) cc_final: 0.8144 (tt0) REVERT: H 68 LYS cc_start: 0.8380 (tttt) cc_final: 0.7950 (ttpp) REVERT: H 80 ASN cc_start: 0.8514 (t0) cc_final: 0.8212 (t0) REVERT: L 18 ASP cc_start: 0.8004 (m-30) cc_final: 0.7764 (m-30) REVERT: L 56 TYR cc_start: 0.8943 (t80) cc_final: 0.8611 (t80) REVERT: L 73 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8628 (p) REVERT: L 91 GLN cc_start: 0.9256 (pp30) cc_final: 0.8375 (pp30) outliers start: 26 outliers final: 22 residues processed: 136 average time/residue: 0.0677 time to fit residues: 11.6698 Evaluate side-chains 135 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.0010 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115983 restraints weight = 7743.841| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.96 r_work: 0.3325 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4745 Z= 0.124 Angle : 0.569 6.875 6448 Z= 0.293 Chirality : 0.042 0.147 739 Planarity : 0.004 0.044 788 Dihedral : 6.573 59.173 705 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.16 % Allowed : 19.25 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.35), residues: 574 helix: 1.39 (0.32), residues: 272 sheet: -0.38 (0.57), residues: 90 loop : -1.31 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 111 TYR 0.011 0.001 TYR A 345 PHE 0.016 0.001 PHE A 268 TRP 0.008 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4740) covalent geometry : angle 0.56786 ( 6440) SS BOND : bond 0.00350 ( 4) SS BOND : angle 0.98164 ( 8) hydrogen bonds : bond 0.04502 ( 263) hydrogen bonds : angle 4.36204 ( 786) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7780 (t80) cc_final: 0.6812 (m-80) REVERT: A 333 THR cc_start: 0.9108 (m) cc_final: 0.8816 (m) REVERT: A 347 ILE cc_start: 0.8644 (mm) cc_final: 0.8378 (mt) REVERT: A 384 TYR cc_start: 0.9015 (t80) cc_final: 0.8714 (t80) REVERT: H 49 GLU cc_start: 0.8454 (tt0) cc_final: 0.8196 (tt0) REVERT: H 68 LYS cc_start: 0.8368 (tttt) cc_final: 0.7927 (ttpp) REVERT: H 80 ASN cc_start: 0.8486 (t0) cc_final: 0.8164 (t0) REVERT: L 18 ASP cc_start: 0.7989 (m-30) cc_final: 0.7737 (m-30) REVERT: L 56 TYR cc_start: 0.8945 (t80) cc_final: 0.8606 (t80) REVERT: L 73 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8604 (p) REVERT: L 91 GLN cc_start: 0.9234 (pp30) cc_final: 0.8286 (pp30) outliers start: 26 outliers final: 23 residues processed: 130 average time/residue: 0.0702 time to fit residues: 11.5691 Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115449 restraints weight = 7878.957| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.00 r_work: 0.3312 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4745 Z= 0.130 Angle : 0.569 6.966 6448 Z= 0.293 Chirality : 0.041 0.135 739 Planarity : 0.004 0.044 788 Dihedral : 6.551 57.126 705 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.56 % Allowed : 20.04 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.35), residues: 574 helix: 1.37 (0.32), residues: 275 sheet: -0.36 (0.57), residues: 90 loop : -1.28 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 111 TYR 0.011 0.001 TYR A 345 PHE 0.016 0.001 PHE A 268 TRP 0.008 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4740) covalent geometry : angle 0.56840 ( 6440) SS BOND : bond 0.00322 ( 4) SS BOND : angle 0.99888 ( 8) hydrogen bonds : bond 0.04531 ( 263) hydrogen bonds : angle 4.36324 ( 786) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7809 (t80) cc_final: 0.6815 (m-80) REVERT: A 271 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: A 305 MET cc_start: 0.8783 (mmm) cc_final: 0.8499 (mtp) REVERT: A 333 THR cc_start: 0.9121 (m) cc_final: 0.8825 (m) REVERT: A 347 ILE cc_start: 0.8716 (mm) cc_final: 0.8456 (mt) REVERT: A 384 TYR cc_start: 0.9000 (t80) cc_final: 0.8679 (t80) REVERT: H 49 GLU cc_start: 0.8426 (tt0) cc_final: 0.8166 (tt0) REVERT: H 68 LYS cc_start: 0.8371 (tttt) cc_final: 0.7921 (ttpp) REVERT: H 80 ASN cc_start: 0.8478 (t0) cc_final: 0.8203 (t0) REVERT: L 18 ASP cc_start: 0.8036 (m-30) cc_final: 0.7763 (m-30) REVERT: L 56 TYR cc_start: 0.8958 (t80) cc_final: 0.8649 (t80) REVERT: L 73 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8621 (p) REVERT: L 91 GLN cc_start: 0.9237 (pp30) cc_final: 0.8294 (pp30) outliers start: 28 outliers final: 23 residues processed: 130 average time/residue: 0.0667 time to fit residues: 11.0169 Evaluate side-chains 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114755 restraints weight = 7744.607| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.98 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4745 Z= 0.138 Angle : 0.586 9.255 6448 Z= 0.301 Chirality : 0.041 0.137 739 Planarity : 0.004 0.043 788 Dihedral : 6.568 56.678 705 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.36 % Allowed : 20.63 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.35), residues: 574 helix: 1.43 (0.32), residues: 273 sheet: -0.35 (0.56), residues: 90 loop : -1.24 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 111 TYR 0.012 0.001 TYR A 345 PHE 0.016 0.001 PHE A 268 TRP 0.011 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4740) covalent geometry : angle 0.58503 ( 6440) SS BOND : bond 0.00315 ( 4) SS BOND : angle 1.01182 ( 8) hydrogen bonds : bond 0.04575 ( 263) hydrogen bonds : angle 4.37626 ( 786) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9102 (mtp-110) cc_final: 0.8894 (mtp85) REVERT: A 333 THR cc_start: 0.9129 (m) cc_final: 0.8830 (m) REVERT: A 347 ILE cc_start: 0.8739 (mm) cc_final: 0.8499 (mt) REVERT: A 384 TYR cc_start: 0.9021 (t80) cc_final: 0.8647 (t80) REVERT: H 49 GLU cc_start: 0.8419 (tt0) cc_final: 0.8165 (tt0) REVERT: H 68 LYS cc_start: 0.8424 (tttt) cc_final: 0.7965 (ttpp) REVERT: H 80 ASN cc_start: 0.8468 (t0) cc_final: 0.8193 (t0) REVERT: L 18 ASP cc_start: 0.8161 (m-30) cc_final: 0.7883 (m-30) REVERT: L 56 TYR cc_start: 0.8974 (t80) cc_final: 0.8644 (t80) REVERT: L 73 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8598 (p) outliers start: 27 outliers final: 24 residues processed: 128 average time/residue: 0.0677 time to fit residues: 10.9415 Evaluate side-chains 136 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 HIS L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116210 restraints weight = 7830.050| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3326 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4745 Z= 0.124 Angle : 0.559 6.989 6448 Z= 0.290 Chirality : 0.041 0.128 739 Planarity : 0.004 0.043 788 Dihedral : 6.487 56.256 705 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.16 % Allowed : 21.63 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.35), residues: 574 helix: 1.53 (0.32), residues: 272 sheet: -0.28 (0.57), residues: 90 loop : -1.11 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 111 TYR 0.011 0.001 TYR A 345 PHE 0.016 0.001 PHE A 268 TRP 0.010 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4740) covalent geometry : angle 0.55876 ( 6440) SS BOND : bond 0.00329 ( 4) SS BOND : angle 0.98434 ( 8) hydrogen bonds : bond 0.04429 ( 263) hydrogen bonds : angle 4.33789 ( 786) Misc. bond : bond 0.00028 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: A 305 MET cc_start: 0.8640 (mtp) cc_final: 0.8193 (mmm) REVERT: A 333 THR cc_start: 0.9140 (m) cc_final: 0.8828 (m) REVERT: A 347 ILE cc_start: 0.8666 (mm) cc_final: 0.8434 (mt) REVERT: A 384 TYR cc_start: 0.9006 (t80) cc_final: 0.8650 (t80) REVERT: H 49 GLU cc_start: 0.8392 (tt0) cc_final: 0.8143 (tt0) REVERT: H 68 LYS cc_start: 0.8379 (tttt) cc_final: 0.7926 (ttpp) REVERT: H 80 ASN cc_start: 0.8466 (t0) cc_final: 0.8186 (t0) REVERT: L 18 ASP cc_start: 0.8067 (m-30) cc_final: 0.7783 (m-30) REVERT: L 56 TYR cc_start: 0.8947 (t80) cc_final: 0.8609 (t80) REVERT: L 73 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8616 (p) outliers start: 26 outliers final: 22 residues processed: 134 average time/residue: 0.0656 time to fit residues: 11.1247 Evaluate side-chains 137 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN H 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115221 restraints weight = 7814.311| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.98 r_work: 0.3316 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4745 Z= 0.132 Angle : 0.573 7.275 6448 Z= 0.296 Chirality : 0.041 0.133 739 Planarity : 0.004 0.043 788 Dihedral : 6.489 56.664 705 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.36 % Allowed : 21.83 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.35), residues: 574 helix: 1.50 (0.32), residues: 272 sheet: -0.24 (0.58), residues: 90 loop : -1.13 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 111 TYR 0.012 0.001 TYR A 360 PHE 0.018 0.001 PHE A 364 TRP 0.008 0.001 TRP L 95 HIS 0.002 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4740) covalent geometry : angle 0.57230 ( 6440) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.02706 ( 8) hydrogen bonds : bond 0.04527 ( 263) hydrogen bonds : angle 4.37345 ( 786) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.05 seconds wall clock time: 21 minutes 10.96 seconds (1270.96 seconds total)