Starting phenix.real_space_refine on Thu Jul 2 02:03:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gye_51693/07_2026/9gye_51693.map" } resolution = 3.5 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= -0.002 sd= 0.013 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 16 5.16 5 C 3481 2.51 5 N 968 2.21 5 O 1035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5502 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5501 Classifications: {'peptide': 686} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 641} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.37, per 1000 atoms: 0.25 Number of scatterers: 5502 At special positions: 0 Unit cell: (67.15, 73.1, 100.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 16 16.00 P 1 15.00 O 1035 8.00 N 968 7.00 C 3481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.46 Conformation dependent library (CDL) restraints added in 206.7 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 7 sheets defined 25.5% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.746A pdb=" N TYR A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 136 through 141 removed outlier: 4.086A pdb=" N VAL A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 141' Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.813A pdb=" N ASN A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.707A pdb=" N TRP A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.728A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.968A pdb=" N LEU A 427 " --> pdb=" O HIS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.791A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 488 removed outlier: 3.946A pdb=" N SER A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.817A pdb=" N GLN A 625 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 626 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 235 removed outlier: 6.570A pdb=" N VAL A 54 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 312 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 56 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 404 " --> pdb=" O CYS A 167 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 165 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 166 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL A 416 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 removed outlier: 6.320A pdb=" N TYR A 103 " --> pdb=" O TYR A 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 526 Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 572 Processing sheet with id=AA6, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 635 163 hydrogen bonds defined for protein. 441 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: 0.80 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1835 1.34 - 1.46: 1180 1.46 - 1.57: 2629 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5671 Sorted by residual: bond pdb=" N MET A 205 " pdb=" CA MET A 205 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.85e+00 bond pdb=" C MET A 205 " pdb=" O MET A 205 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.19e-02 7.06e+03 1.79e+00 bond pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.26e+00 bond pdb=" C VAL A 250 " pdb=" O VAL A 250 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 bond pdb=" CA MET A 289 " pdb=" CB MET A 289 " ideal model delta sigma weight residual 1.528 1.512 0.017 1.51e-02 4.39e+03 1.24e+00 ... (remaining 5666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7496 1.79 - 3.58: 189 3.58 - 5.38: 40 5.38 - 7.17: 8 7.17 - 8.96: 5 Bond angle restraints: 7738 Sorted by residual: angle pdb=" CA LYS A 494 " pdb=" CB LYS A 494 " pdb=" CG LYS A 494 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.46e+00 angle pdb=" N ASN A 704 " pdb=" CA ASN A 704 " pdb=" CB ASN A 704 " ideal model delta sigma weight residual 113.65 109.39 4.26 1.47e+00 4.63e-01 8.40e+00 angle pdb=" CB LYS A 494 " pdb=" CG LYS A 494 " pdb=" CD LYS A 494 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " ideal model delta sigma weight residual 110.49 115.28 -4.79 1.69e+00 3.50e-01 8.02e+00 ... (remaining 7733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2805 17.48 - 34.97: 371 34.97 - 52.45: 79 52.45 - 69.93: 29 69.93 - 87.41: 11 Dihedral angle restraints: 3295 sinusoidal: 1311 harmonic: 1984 Sorted by residual: dihedral pdb=" CA ALA A 288 " pdb=" C ALA A 288 " pdb=" N MET A 289 " pdb=" CA MET A 289 " ideal model delta harmonic sigma weight residual -180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLN A 625 " pdb=" C GLN A 625 " pdb=" N MET A 626 " pdb=" CA MET A 626 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TYR A 518 " pdb=" C TYR A 518 " pdb=" N GLN A 519 " pdb=" CA GLN A 519 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 3292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 643 0.060 - 0.120: 129 0.120 - 0.180: 10 0.180 - 0.239: 1 0.239 - 0.299: 1 Chirality restraints: 784 Sorted by residual: chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA LYS A 97 " pdb=" N LYS A 97 " pdb=" C LYS A 97 " pdb=" CB LYS A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 781 not shown) Planarity restraints: 1025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 674 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 675 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 257 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ARG A 257 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 257 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 258 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 246 " -0.009 2.00e-02 2.50e+03 9.68e-03 2.34e+00 pdb=" CG TRP A 246 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 246 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 246 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 246 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 246 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 246 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 246 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 246 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 246 " 0.000 2.00e-02 2.50e+03 ... (remaining 1022 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 157 2.66 - 3.22: 5288 3.22 - 3.78: 8896 3.78 - 4.34: 11810 4.34 - 4.90: 19469 Nonbonded interactions: 45620 Sorted by model distance: nonbonded pdb=" OH TYR A 249 " pdb=" OH TYR A 264 " model vdw 2.094 3.040 nonbonded pdb=" OD1 ASN A 61 " pdb=" OD2 ASP A 360 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASP A 231 " pdb=" NH1 ARG A 287 " model vdw 2.120 3.120 nonbonded pdb=" NE2 GLN A 236 " pdb=" O GLY A 238 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR A 110 " pdb=" O PRO A 491 " model vdw 2.168 3.040 ... (remaining 45615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.190 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.340 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.004 0.031 5671 Z= 0.192 Angle : 0.737 8.961 7738 Z= 0.383 Chirality : 0.048 0.299 784 Planarity : 0.005 0.050 1025 Dihedral : 17.510 87.415 2035 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.17 % Allowed : 30.43 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.33), residues: 681 helix: 0.41 (0.47), residues: 126 sheet: 0.40 (0.41), residues: 174 loop : -0.54 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.021 0.002 TYR A 318 PHE 0.008 0.001 PHE A 352 TRP 0.026 0.002 TRP A 246 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 5671) covalent geometry : angle 0.73737 / 0.38 ( 7738) hydrogen bonds : bond 0.14976 / 10.04 ( 163) hydrogen bonds : angle 7.24828 / 5.09 ( 441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.214 Fit side-chains REVERT: A 58 MET cc_start: 0.7903 (ttt) cc_final: 0.7643 (ttm) REVERT: A 146 MET cc_start: 0.7277 (mmm) cc_final: 0.7041 (mmm) REVERT: A 237 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6274 (mm-30) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.0554 time to fit residues: 4.2955 Evaluate side-chains 38 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 HIS ** A 475 GLN ** 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 = 0.3122 r_free = 0.3122 target = 0.053615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044043 restraints weight = 24518.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.045834 restraints weight = 12166.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047113 restraints weight = 7518.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048042 restraints weight = 5264.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048695 restraints weight = 4005.396| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5671 Z= 0.140 Angle : 0.617 7.111 7738 Z= 0.316 Chirality : 0.045 0.234 784 Planarity : 0.005 0.041 1025 Dihedral : 5.103 57.929 771 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.65 % Allowed : 28.00 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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 (0.33), residues: 681 helix: 0.87 (0.48), residues: 125 sheet: 0.61 (0.41), residues: 171 loop : -0.44 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.020 0.002 TYR A 692 PHE 0.013 0.001 PHE A 68 TRP 0.015 0.001 TRP A 122 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5671) covalent geometry : angle 0.61652 / 0.32 ( 7738) hydrogen bonds : bond 0.03622 / 2.52 ( 163) hydrogen bonds : angle 5.67215 / 4.02 ( 441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8556 (ttt) cc_final: 0.8271 (ttp) REVERT: A 146 MET cc_start: 0.8244 (mmm) cc_final: 0.7321 (mmm) REVERT: A 313 VAL cc_start: 0.9635 (t) cc_final: 0.9315 (p) REVERT: A 496 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6616 (m-90) REVERT: A 557 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8181 (mp10) outliers start: 21 outliers final: 7 residues processed: 58 average time/residue: 0.0618 time to fit residues: 5.0929 Evaluate side-chains 44 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 587 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS A 172 GLN A 262 ASN A 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.043205 restraints weight = 24972.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044939 restraints weight = 12522.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046181 restraints weight = 7835.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047094 restraints weight = 5503.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.047664 restraints weight = 4215.975| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5671 Z= 0.165 Angle : 0.573 5.963 7738 Z= 0.296 Chirality : 0.045 0.211 784 Planarity : 0.004 0.053 1025 Dihedral : 5.037 58.151 771 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.35 % Allowed : 23.65 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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 (0.34), residues: 681 helix: 0.69 (0.47), residues: 137 sheet: 0.63 (0.41), residues: 171 loop : -0.40 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 189 TYR 0.020 0.002 TYR A 692 PHE 0.018 0.001 PHE A 100 TRP 0.015 0.001 TRP A 122 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5671) covalent geometry : angle 0.57253 / 0.30 ( 7738) hydrogen bonds : bond 0.03169 / 2.25 ( 163) hydrogen bonds : angle 5.39321 / 3.83 ( 441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 122 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7453 (t-100) REVERT: A 146 MET cc_start: 0.8368 (mmm) cc_final: 0.7385 (mmm) REVERT: A 292 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7558 (ttt90) REVERT: A 313 VAL cc_start: 0.9594 (t) cc_final: 0.9220 (p) REVERT: A 332 TYR cc_start: 0.9128 (t80) cc_final: 0.8700 (t80) REVERT: A 357 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (p0) REVERT: A 496 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.6722 (m-90) REVERT: A 540 ASP cc_start: 0.8306 (t0) cc_final: 0.8059 (t0) REVERT: A 720 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7494 (mtp85) outliers start: 25 outliers final: 9 residues processed: 59 average time/residue: 0.0670 time to fit residues: 5.5145 Evaluate side-chains 49 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.052944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.043712 restraints weight = 24508.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045440 restraints weight = 12031.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046733 restraints weight = 7448.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047651 restraints weight = 5176.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048314 restraints weight = 3918.873| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5671 Z= 0.126 Angle : 0.543 7.757 7738 Z= 0.276 Chirality : 0.044 0.148 784 Planarity : 0.004 0.055 1025 Dihedral : 4.870 57.992 771 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.00 % Allowed : 24.00 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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 (0.34), residues: 681 helix: 0.84 (0.47), residues: 137 sheet: 0.79 (0.42), residues: 167 loop : -0.42 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.023 0.001 TYR A 692 PHE 0.016 0.001 PHE A 100 TRP 0.015 0.001 TRP A 122 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 5671) covalent geometry : angle 0.54260 / 0.28 ( 7738) hydrogen bonds : bond 0.02839 / 1.99 ( 163) hydrogen bonds : angle 5.19598 / 3.69 ( 441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7740 (tt0) cc_final: 0.7491 (tt0) REVERT: A 122 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7454 (t-100) REVERT: A 125 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8686 (t80) REVERT: A 146 MET cc_start: 0.8305 (mmm) cc_final: 0.7243 (mmm) REVERT: A 289 MET cc_start: 0.5877 (ttt) cc_final: 0.5567 (ttt) REVERT: A 292 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7563 (ttt90) REVERT: A 332 TYR cc_start: 0.9173 (t80) cc_final: 0.8714 (t80) REVERT: A 496 TRP cc_start: 0.7716 (OUTLIER) cc_final: 0.6678 (m-90) REVERT: A 507 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8654 (mm-30) REVERT: A 540 ASP cc_start: 0.8341 (t0) cc_final: 0.8032 (t0) REVERT: A 557 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: A 720 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7571 (mtp85) outliers start: 23 outliers final: 9 residues processed: 56 average time/residue: 0.0664 time to fit residues: 5.1944 Evaluate side-chains 51 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.043447 restraints weight = 25434.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045205 restraints weight = 12533.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046477 restraints weight = 7775.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047379 restraints weight = 5416.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048063 restraints weight = 4131.854| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5671 Z= 0.125 Angle : 0.533 6.815 7738 Z= 0.271 Chirality : 0.043 0.138 784 Planarity : 0.004 0.055 1025 Dihedral : 4.744 57.663 771 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.35 % Allowed : 23.30 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.30 (0.34), residues: 681 helix: 0.90 (0.47), residues: 137 sheet: 0.89 (0.42), residues: 167 loop : -0.35 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.023 0.001 TYR A 692 PHE 0.009 0.001 PHE A 64 TRP 0.015 0.001 TRP A 122 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5671) covalent geometry : angle 0.53255 / 0.27 ( 7738) hydrogen bonds : bond 0.02693 / 1.89 ( 163) hydrogen bonds : angle 5.04958 / 3.58 ( 441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7320 (t-100) REVERT: A 125 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8717 (t80) REVERT: A 146 MET cc_start: 0.8382 (mmm) cc_final: 0.8013 (mmm) REVERT: A 184 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 292 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7667 (ttt90) REVERT: A 332 TYR cc_start: 0.9217 (t80) cc_final: 0.8739 (t80) REVERT: A 494 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7894 (mmtt) REVERT: A 496 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.6721 (m-90) REVERT: A 507 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8701 (mm-30) REVERT: A 540 ASP cc_start: 0.8439 (t0) cc_final: 0.8061 (t0) REVERT: A 557 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: A 720 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7627 (mtp85) outliers start: 25 outliers final: 12 residues processed: 57 average time/residue: 0.0697 time to fit residues: 5.5139 Evaluate side-chains 53 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 33 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 41 optimal weight: 0.0040 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.042036 restraints weight = 25402.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043726 restraints weight = 12422.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044953 restraints weight = 7667.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045762 restraints weight = 5338.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046397 restraints weight = 4091.300| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5671 Z= 0.198 Angle : 0.570 6.391 7738 Z= 0.291 Chirality : 0.046 0.361 784 Planarity : 0.004 0.050 1025 Dihedral : 4.926 57.468 771 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.87 % Allowed : 22.61 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.23 (0.35), residues: 681 helix: 0.72 (0.47), residues: 143 sheet: 0.65 (0.44), residues: 158 loop : -0.21 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 189 TYR 0.023 0.002 TYR A 692 PHE 0.009 0.001 PHE A 556 TRP 0.017 0.001 TRP A 122 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 5671) covalent geometry : angle 0.56965 / 0.29 ( 7738) hydrogen bonds : bond 0.03075 / 2.18 ( 163) hydrogen bonds : angle 5.23037 / 3.70 ( 441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 29 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 122 TRP cc_start: 0.8137 (OUTLIER) cc_final: 0.7303 (t-100) REVERT: A 125 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8740 (t80) REVERT: A 174 MET cc_start: 0.8541 (tmm) cc_final: 0.8201 (tmm) REVERT: A 292 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8116 (ttt180) REVERT: A 496 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6723 (m-90) REVERT: A 507 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8650 (mm-30) REVERT: A 540 ASP cc_start: 0.8492 (t0) cc_final: 0.8078 (t0) REVERT: A 557 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8090 (mp10) outliers start: 28 outliers final: 15 residues processed: 55 average time/residue: 0.0683 time to fit residues: 5.2673 Evaluate side-chains 50 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 28 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 57 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.051721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.042534 restraints weight = 25777.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.044255 restraints weight = 12693.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045475 restraints weight = 7850.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046400 restraints weight = 5472.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047038 restraints weight = 4120.088| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5671 Z= 0.151 Angle : 0.556 7.311 7738 Z= 0.283 Chirality : 0.045 0.285 784 Planarity : 0.004 0.050 1025 Dihedral : 4.841 57.208 771 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.87 % Allowed : 23.13 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.17 (0.34), residues: 681 helix: 0.77 (0.47), residues: 143 sheet: 0.66 (0.43), residues: 166 loop : -0.35 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.025 0.001 TYR A 692 PHE 0.007 0.001 PHE A 64 TRP 0.016 0.001 TRP A 122 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 5671) covalent geometry : angle 0.55583 / 0.28 ( 7738) hydrogen bonds : bond 0.02851 / 2.02 ( 163) hydrogen bonds : angle 5.10845 / 3.62 ( 441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 58 MET cc_start: 0.7958 (ttm) cc_final: 0.7747 (ttm) REVERT: A 122 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.7329 (t-100) REVERT: A 125 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8771 (t80) REVERT: A 138 MET cc_start: 0.8449 (mtp) cc_final: 0.8188 (ttm) REVERT: A 146 MET cc_start: 0.8105 (mmm) cc_final: 0.7339 (mmm) REVERT: A 184 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.8205 (t80) REVERT: A 286 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8985 (pt0) REVERT: A 292 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8203 (ttt180) REVERT: A 496 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.6764 (m-90) REVERT: A 507 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: A 540 ASP cc_start: 0.8497 (t0) cc_final: 0.8062 (t0) REVERT: A 557 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8106 (mp10) outliers start: 28 outliers final: 15 residues processed: 57 average time/residue: 0.0773 time to fit residues: 5.9727 Evaluate side-chains 54 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 30 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.0070 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 0.0470 chunk 42 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 overall best weight: 0.8498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.052921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043755 restraints weight = 24557.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.045515 restraints weight = 11948.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046800 restraints weight = 7322.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047676 restraints weight = 5043.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048359 restraints weight = 3778.995| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5671 Z= 0.095 Angle : 0.540 7.239 7738 Z= 0.271 Chirality : 0.044 0.242 784 Planarity : 0.004 0.051 1025 Dihedral : 4.575 56.167 771 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.13 % Allowed : 25.04 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.25 (0.34), residues: 681 helix: 0.83 (0.47), residues: 143 sheet: 0.80 (0.43), residues: 166 loop : -0.34 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.024 0.001 TYR A 692 PHE 0.009 0.001 PHE A 64 TRP 0.019 0.001 TRP A 246 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 5671) covalent geometry : angle 0.54039 / 0.27 ( 7738) hydrogen bonds : bond 0.02514 / 1.78 ( 163) hydrogen bonds : angle 4.85543 / 3.45 ( 441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 122 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.6985 (t-100) REVERT: A 125 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8755 (t80) REVERT: A 174 MET cc_start: 0.8476 (tmm) cc_final: 0.7981 (ppp) REVERT: A 184 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 292 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7737 (mtt90) REVERT: A 332 TYR cc_start: 0.9313 (t80) cc_final: 0.8782 (t80) REVERT: A 356 TYR cc_start: 0.8995 (m-80) cc_final: 0.8488 (m-80) REVERT: A 496 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.6704 (m-90) REVERT: A 507 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8750 (mm-30) REVERT: A 540 ASP cc_start: 0.8458 (t0) cc_final: 0.8053 (t0) outliers start: 18 outliers final: 9 residues processed: 51 average time/residue: 0.0700 time to fit residues: 5.0142 Evaluate side-chains 48 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.042112 restraints weight = 25405.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043837 restraints weight = 12482.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045016 restraints weight = 7685.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.045917 restraints weight = 5371.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.046557 restraints weight = 4058.335| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5671 Z= 0.178 Angle : 0.570 7.261 7738 Z= 0.290 Chirality : 0.045 0.250 784 Planarity : 0.004 0.048 1025 Dihedral : 4.785 56.524 771 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.65 % Allowed : 24.52 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.11 (0.34), residues: 681 helix: 0.83 (0.48), residues: 143 sheet: 0.73 (0.45), residues: 146 loop : -0.44 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.024 0.001 TYR A 692 PHE 0.011 0.001 PHE A 100 TRP 0.017 0.001 TRP A 122 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 ( 5671) covalent geometry : angle 0.57031 / 0.29 ( 7738) hydrogen bonds : bond 0.02878 / 2.04 ( 163) hydrogen bonds : angle 5.06659 / 3.59 ( 441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 122 TRP cc_start: 0.8115 (OUTLIER) cc_final: 0.7264 (t-100) REVERT: A 125 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8843 (t80) REVERT: A 138 MET cc_start: 0.8180 (ttm) cc_final: 0.7955 (ttm) REVERT: A 146 MET cc_start: 0.8143 (mmm) cc_final: 0.7334 (mmm) REVERT: A 184 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8214 (t80) REVERT: A 289 MET cc_start: 0.6072 (ttt) cc_final: 0.5809 (ttt) REVERT: A 292 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8247 (ttt180) REVERT: A 496 TRP cc_start: 0.7640 (OUTLIER) cc_final: 0.6782 (m-90) REVERT: A 507 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8721 (mm-30) REVERT: A 540 ASP cc_start: 0.8519 (t0) cc_final: 0.8093 (t0) outliers start: 21 outliers final: 11 residues processed: 51 average time/residue: 0.0715 time to fit residues: 5.0541 Evaluate side-chains 49 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.050874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.041858 restraints weight = 25935.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043546 restraints weight = 12702.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.044739 restraints weight = 7846.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045607 restraints weight = 5461.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046233 restraints weight = 4145.147| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5671 Z= 0.213 Angle : 0.608 7.555 7738 Z= 0.310 Chirality : 0.046 0.253 784 Planarity : 0.004 0.047 1025 Dihedral : 5.036 57.142 771 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.48 % Allowed : 24.87 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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 (0.34), residues: 681 helix: 0.91 (0.48), residues: 137 sheet: 0.53 (0.45), residues: 146 loop : -0.58 (0.34), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 650 TYR 0.025 0.002 TYR A 692 PHE 0.013 0.001 PHE A 100 TRP 0.018 0.002 TRP A 122 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 ( 5671) covalent geometry : angle 0.60791 / 0.31 ( 7738) hydrogen bonds : bond 0.03124 / 2.20 ( 163) hydrogen bonds : angle 5.25623 / 3.78 ( 441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8484 (tt) REVERT: A 122 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7257 (t-100) REVERT: A 125 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8829 (t80) REVERT: A 174 MET cc_start: 0.8583 (tmm) cc_final: 0.8262 (tmm) REVERT: A 184 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 496 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.6925 (m-90) REVERT: A 507 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: A 540 ASP cc_start: 0.8494 (t0) cc_final: 0.8050 (t0) REVERT: A 542 MET cc_start: 0.8034 (tpt) cc_final: 0.7719 (tpp) REVERT: A 557 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8166 (mp10) outliers start: 20 outliers final: 13 residues processed: 50 average time/residue: 0.0614 time to fit residues: 4.3780 Evaluate side-chains 50 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 122 TRP Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 720 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.042011 restraints weight = 25168.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043683 restraints weight = 12381.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.044881 restraints weight = 7639.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.045740 restraints weight = 5290.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046392 restraints weight = 4010.556| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5671 Z= 0.175 Angle : 0.588 7.489 7738 Z= 0.299 Chirality : 0.045 0.238 784 Planarity : 0.004 0.046 1025 Dihedral : 4.988 56.898 771 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.65 % Allowed : 24.70 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.08 (0.34), residues: 681 helix: 0.93 (0.48), residues: 137 sheet: 0.64 (0.45), residues: 142 loop : -0.65 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 646 TYR 0.025 0.001 TYR A 692 PHE 0.019 0.001 PHE A 100 TRP 0.017 0.001 TRP A 122 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 5671) covalent geometry : angle 0.58818 / 0.30 ( 7738) hydrogen bonds : bond 0.02963 / 2.09 ( 163) hydrogen bonds : angle 5.22398 / 3.76 ( 441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.49 seconds wall clock time: 19 minutes 6.03 seconds (1146.03 seconds total)