Starting phenix.real_space_refine on Tue Aug 4 16:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrt_37789/08_2026/8wrt_37789.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 8 5.16 5 C 2954 2.51 5 N 884 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4812 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4267 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 35, 'TRANS': 494} Chain breaks: 7 Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pyr': 5, 'rna3p_pur': 9, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 20} Time building chain proxies: 1.35, per 1000 atoms: 0.28 Number of scatterers: 4812 At special positions: 0 Unit cell: (76.56, 85.14, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 26 15.00 O 940 8.00 N 884 7.00 C 2954 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: 0.41 Conformation dependent library (CDL) restraints added in 145.7 milliseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 2 sheets defined 48.7% alpha, 7.7% beta 3 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 87 removed outlier: 3.696A pdb=" N GLY A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 removed outlier: 3.838A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.567A pdb=" N LEU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 169 removed outlier: 3.575A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.844A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.524A pdb=" N HIS A 253 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 254 " --> pdb=" O ARG A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 254' Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.925A pdb=" N ARG A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.556A pdb=" N ALA A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.804A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 451 removed outlier: 3.807A pdb=" N THR A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 4.184A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.527A pdb=" N LEU A 475 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.881A pdb=" N SER A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 removed outlier: 3.637A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 587 removed outlier: 3.510A pdb=" N VAL A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 removed outlier: 3.931A pdb=" N PHE A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 618 " --> pdb=" O TRP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 641 removed outlier: 4.096A pdb=" N ALA A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 4.476A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419 removed outlier: 6.112A pdb=" N PHE A 401 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN A 418 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA A 399 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 400 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 388 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 7 hydrogen bonds 14 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1337 1.33 - 1.45: 911 1.45 - 1.57: 2659 1.57 - 1.69: 51 1.69 - 1.81: 11 Bond restraints: 4969 Sorted by residual: bond pdb=" C ARG A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.51e+00 bond pdb=" CA ARG A 536 " pdb=" C ARG A 536 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.19e-02 7.06e+03 4.96e+00 bond pdb=" CA HIS A 214 " pdb=" C HIS A 214 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.26e-02 6.30e+03 4.04e+00 bond pdb=" C LEU A 228 " pdb=" N PRO A 229 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.25e-02 6.40e+03 3.85e+00 bond pdb=" C SER A 466 " pdb=" O SER A 466 " ideal model delta sigma weight residual 1.235 1.217 0.019 1.26e-02 6.30e+03 2.18e+00 ... (remaining 4964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6549 1.90 - 3.79: 255 3.79 - 5.69: 28 5.69 - 7.59: 4 7.59 - 9.49: 2 Bond angle restraints: 6838 Sorted by residual: angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 119.70 124.61 -4.91 1.20e+00 6.94e-01 1.67e+01 angle pdb=" N ARG A 406 " pdb=" CA ARG A 406 " pdb=" C ARG A 406 " ideal model delta sigma weight residual 110.50 116.12 -5.62 1.41e+00 5.03e-01 1.59e+01 angle pdb=" C3' U B -9 " pdb=" O3' U B -9 " pdb=" P C B -8 " ideal model delta sigma weight residual 119.70 124.40 -4.70 1.20e+00 6.94e-01 1.54e+01 angle pdb=" N ARG A 251 " pdb=" CA ARG A 251 " pdb=" C ARG A 251 " ideal model delta sigma weight residual 112.75 117.98 -5.23 1.36e+00 5.41e-01 1.48e+01 angle pdb=" O5' C B -19 " pdb=" C5' C B -19 " pdb=" C4' C B -19 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.48e+01 ... (remaining 6833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 2936 35.27 - 70.53: 120 70.53 - 105.80: 15 105.80 - 141.06: 0 141.06 - 176.33: 3 Dihedral angle restraints: 3074 sinusoidal: 1549 harmonic: 1525 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual -128.00 48.33 -176.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B -8 " pdb=" C1' C B -8 " pdb=" N1 C B -8 " pdb=" C2 C B -8 " ideal model delta sinusoidal sigma weight residual -128.00 -47.56 -80.44 1 1.70e+01 3.46e-03 2.77e+01 dihedral pdb=" C4' C B -8 " pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sinusoidal sigma weight residual 250.00 74.08 175.92 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 3071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 624 0.060 - 0.119: 107 0.119 - 0.179: 33 0.179 - 0.239: 3 0.239 - 0.299: 1 Chirality restraints: 768 Sorted by residual: chirality pdb=" CA ARG A 251 " pdb=" N ARG A 251 " pdb=" C ARG A 251 " pdb=" CB ARG A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ALA A 216 " pdb=" N ALA A 216 " pdb=" C ALA A 216 " pdb=" CB ALA A 216 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 218 " pdb=" N PRO A 218 " pdb=" C PRO A 218 " pdb=" CB PRO A 218 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 765 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 238 " -0.091 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO A 239 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 214 " 0.056 5.00e-02 4.00e+02 8.43e-02 1.14e+01 pdb=" N PRO A 215 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 273 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 274 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.026 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1280 2.81 - 3.33: 4515 3.33 - 3.85: 7720 3.85 - 4.38: 8885 4.38 - 4.90: 14148 Nonbonded interactions: 36548 Sorted by model distance: nonbonded pdb=" O2' C B 0 " pdb=" OP1 C B 2 " model vdw 2.287 3.040 nonbonded pdb=" NH2 ARG A 139 " pdb=" O3' C B 4 " model vdw 2.333 3.120 nonbonded pdb=" O THR A 583 " pdb=" OG1 THR A 587 " model vdw 2.412 3.040 nonbonded pdb=" O LEU A 416 " pdb=" NE1 TRP A 586 " model vdw 2.426 3.120 nonbonded pdb=" O VAL A 547 " pdb=" OG1 THR A 551 " model vdw 2.449 3.040 ... (remaining 36543 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: 6.020 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.860 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 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 : 0.003 0.052 4969 Z= 0.204 Angle : 0.782 9.487 6838 Z= 0.499 Chirality : 0.051 0.299 768 Planarity : 0.008 0.136 785 Dihedral : 18.166 176.326 2084 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.44 % Allowed : 1.75 % Favored : 97.81 % 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: -0.94 (0.36), residues: 514 helix: 0.11 (0.33), residues: 211 sheet: -2.37 (0.66), residues: 54 loop : -0.74 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.011 0.001 TYR A 578 PHE 0.015 0.002 PHE A 335 TRP 0.018 0.001 TRP A 626 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.20 ( 4969) covalent geometry : angle 0.78246 / 0.50 ( 6838) hydrogen bonds : bond 0.25320 / 18.17 ( 180) hydrogen bonds : angle 8.40816 / 6.16 ( 506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7323 (tmt-80) cc_final: 0.6837 (tpt170) REVERT: A 308 ASP cc_start: 0.6394 (m-30) cc_final: 0.6101 (m-30) REVERT: A 371 LYS cc_start: 0.6434 (mppt) cc_final: 0.6008 (tmtt) REVERT: A 571 LEU cc_start: 0.7001 (mt) cc_final: 0.6799 (mt) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1323 time to fit residues: 11.4874 Evaluate side-chains 68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.182910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.160694 restraints weight = 7789.166| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.35 r_work: 0.3948 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4969 Z= 0.217 Angle : 0.698 7.750 6838 Z= 0.367 Chirality : 0.049 0.390 768 Planarity : 0.007 0.090 785 Dihedral : 20.758 177.857 1006 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.44 % Allowed : 8.99 % Favored : 90.57 % 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: -0.85 (0.36), residues: 514 helix: 0.12 (0.32), residues: 217 sheet: -2.36 (0.66), residues: 51 loop : -0.65 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 251 TYR 0.027 0.003 TYR A 123 PHE 0.024 0.002 PHE A 335 TRP 0.015 0.002 TRP A 112 HIS 0.008 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 ( 4969) covalent geometry : angle 0.69798 / 0.37 ( 6838) hydrogen bonds : bond 0.06621 / 4.50 ( 180) hydrogen bonds : angle 5.35697 / 3.81 ( 506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7421 (tmt-80) cc_final: 0.7159 (tpt90) REVERT: A 308 ASP cc_start: 0.6965 (m-30) cc_final: 0.6617 (m-30) REVERT: A 371 LYS cc_start: 0.6797 (mppt) cc_final: 0.6032 (tmtt) REVERT: A 578 TYR cc_start: 0.6382 (t80) cc_final: 0.6063 (t80) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.1294 time to fit residues: 10.3384 Evaluate side-chains 64 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 20 optimal weight: 0.0670 chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.184518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161983 restraints weight = 7661.961| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.41 r_work: 0.3961 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4969 Z= 0.133 Angle : 0.599 7.137 6838 Z= 0.311 Chirality : 0.045 0.376 768 Planarity : 0.006 0.067 785 Dihedral : 20.715 177.377 1004 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.32 % Allowed : 13.38 % Favored : 85.31 % 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: -0.53 (0.37), residues: 514 helix: 0.49 (0.33), residues: 223 sheet: -2.31 (0.62), residues: 56 loop : -0.55 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262 TYR 0.023 0.002 TYR A 432 PHE 0.021 0.001 PHE A 102 TRP 0.016 0.002 TRP A 112 HIS 0.007 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4969) covalent geometry : angle 0.59857 / 0.31 ( 6838) hydrogen bonds : bond 0.05077 / 3.44 ( 180) hydrogen bonds : angle 4.67988 / 3.34 ( 506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7331 (tmt-80) cc_final: 0.7000 (tpt170) REVERT: A 150 ARG cc_start: 0.7422 (mtm180) cc_final: 0.6768 (ttp-170) REVERT: A 166 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6331 (tm-30) REVERT: A 308 ASP cc_start: 0.6953 (m-30) cc_final: 0.6650 (m-30) REVERT: A 371 LYS cc_start: 0.6786 (mppt) cc_final: 0.5993 (tmtt) REVERT: A 444 LYS cc_start: 0.8247 (tmmt) cc_final: 0.7988 (tmmt) REVERT: A 578 TYR cc_start: 0.6425 (t80) cc_final: 0.6138 (t80) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 0.1384 time to fit residues: 10.9345 Evaluate side-chains 65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.183205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161360 restraints weight = 7704.351| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.37 r_work: 0.3949 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4969 Z= 0.161 Angle : 0.601 7.230 6838 Z= 0.315 Chirality : 0.045 0.380 768 Planarity : 0.005 0.058 785 Dihedral : 20.701 178.086 1004 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.75 % Allowed : 14.47 % Favored : 83.77 % 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: -0.43 (0.37), residues: 514 helix: 0.63 (0.33), residues: 223 sheet: -2.14 (0.63), residues: 56 loop : -0.59 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.024 0.003 TYR A 123 PHE 0.022 0.002 PHE A 102 TRP 0.018 0.002 TRP A 614 HIS 0.009 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 4969) covalent geometry : angle 0.60132 / 0.31 ( 6838) hydrogen bonds : bond 0.04720 / 3.12 ( 180) hydrogen bonds : angle 4.45795 / 3.16 ( 506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7322 (tmt-80) cc_final: 0.6928 (tpt170) REVERT: A 166 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6481 (tm-30) REVERT: A 308 ASP cc_start: 0.7000 (m-30) cc_final: 0.6637 (m-30) REVERT: A 371 LYS cc_start: 0.6856 (mppt) cc_final: 0.6066 (tmtt) REVERT: A 441 GLU cc_start: 0.7913 (mp0) cc_final: 0.7543 (mp0) REVERT: A 578 TYR cc_start: 0.6475 (t80) cc_final: 0.6124 (t80) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.1320 time to fit residues: 10.7773 Evaluate side-chains 65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.182934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.160670 restraints weight = 7757.997| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.41 r_work: 0.3945 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4969 Z= 0.174 Angle : 0.619 7.299 6838 Z= 0.323 Chirality : 0.046 0.384 768 Planarity : 0.006 0.057 785 Dihedral : 20.738 178.249 1004 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.32 % Allowed : 16.67 % Favored : 82.02 % 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: -0.42 (0.37), residues: 514 helix: 0.74 (0.33), residues: 224 sheet: -2.11 (0.63), residues: 56 loop : -0.71 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.026 0.003 TYR A 432 PHE 0.022 0.002 PHE A 102 TRP 0.016 0.002 TRP A 485 HIS 0.013 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 4969) covalent geometry : angle 0.61859 / 0.32 ( 6838) hydrogen bonds : bond 0.04542 / 3.04 ( 180) hydrogen bonds : angle 4.36567 / 3.08 ( 506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7365 (tmt-80) cc_final: 0.6866 (tpt170) REVERT: A 441 GLU cc_start: 0.7930 (mp0) cc_final: 0.7689 (mp0) REVERT: A 485 TRP cc_start: 0.5340 (OUTLIER) cc_final: 0.4921 (t-100) REVERT: A 578 TYR cc_start: 0.6471 (t80) cc_final: 0.6110 (t80) REVERT: A 633 LYS cc_start: 0.6354 (ptmm) cc_final: 0.5909 (tptp) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.1221 time to fit residues: 10.1896 Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 0.0040 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.185440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162832 restraints weight = 7845.050| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.40 r_work: 0.3976 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4969 Z= 0.144 Angle : 0.589 7.238 6838 Z= 0.306 Chirality : 0.045 0.381 768 Planarity : 0.006 0.066 785 Dihedral : 20.721 178.412 1004 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.75 % Allowed : 17.98 % Favored : 80.26 % 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 (0.38), residues: 514 helix: 0.99 (0.34), residues: 220 sheet: -2.04 (0.63), residues: 56 loop : -0.65 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.025 0.002 TYR A 432 PHE 0.025 0.001 PHE A 102 TRP 0.024 0.002 TRP A 485 HIS 0.009 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 4969) covalent geometry : angle 0.58881 / 0.31 ( 6838) hydrogen bonds : bond 0.04194 / 2.80 ( 180) hydrogen bonds : angle 4.25072 / 3.01 ( 506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7334 (tmt-80) cc_final: 0.7026 (tpt90) REVERT: A 441 GLU cc_start: 0.7913 (mp0) cc_final: 0.7687 (mp0) REVERT: A 578 TYR cc_start: 0.6457 (t80) cc_final: 0.6137 (t80) REVERT: A 633 LYS cc_start: 0.6356 (ptmm) cc_final: 0.5932 (tptp) outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.1325 time to fit residues: 10.6495 Evaluate side-chains 66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 = 0.4344 r_free = 0.4344 target = 0.183912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161742 restraints weight = 7646.604| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.34 r_work: 0.3954 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4969 Z= 0.174 Angle : 0.619 8.292 6838 Z= 0.319 Chirality : 0.046 0.386 768 Planarity : 0.006 0.055 785 Dihedral : 20.751 178.246 1004 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.10 % Allowed : 19.30 % Favored : 79.61 % 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: -0.30 (0.38), residues: 514 helix: 0.89 (0.34), residues: 226 sheet: -2.04 (0.62), residues: 56 loop : -0.72 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 262 TYR 0.021 0.003 TYR A 432 PHE 0.025 0.001 PHE A 102 TRP 0.042 0.003 TRP A 485 HIS 0.013 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 4969) covalent geometry : angle 0.61867 / 0.32 ( 6838) hydrogen bonds : bond 0.04347 / 2.91 ( 180) hydrogen bonds : angle 4.29843 / 2.98 ( 506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7351 (tmt-80) cc_final: 0.7066 (tpt90) REVERT: A 262 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6910 (ttp80) REVERT: A 578 TYR cc_start: 0.6502 (t80) cc_final: 0.6131 (t80) REVERT: A 633 LYS cc_start: 0.6379 (ptmm) cc_final: 0.5946 (tptp) outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 0.1355 time to fit residues: 10.8147 Evaluate side-chains 66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 = 0.4335 r_free = 0.4335 target = 0.183089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161151 restraints weight = 7663.823| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 2.28 r_work: 0.3961 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4969 Z= 0.191 Angle : 0.665 7.956 6838 Z= 0.347 Chirality : 0.047 0.388 768 Planarity : 0.006 0.054 785 Dihedral : 20.767 178.269 1004 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.54 % Allowed : 19.96 % Favored : 78.51 % 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: -0.38 (0.38), residues: 514 helix: 0.87 (0.33), residues: 222 sheet: -2.06 (0.63), residues: 56 loop : -0.81 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 262 TYR 0.025 0.003 TYR A 432 PHE 0.022 0.002 PHE A 102 TRP 0.040 0.003 TRP A 614 HIS 0.011 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 4969) covalent geometry : angle 0.66486 / 0.35 ( 6838) hydrogen bonds : bond 0.04364 / 2.91 ( 180) hydrogen bonds : angle 4.36028 / 3.01 ( 506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7186 (mp0) cc_final: 0.6946 (mp0) REVERT: A 96 ARG cc_start: 0.7292 (tmt-80) cc_final: 0.7024 (tpt90) REVERT: A 262 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6916 (ttp80) REVERT: A 441 GLU cc_start: 0.7646 (mp0) cc_final: 0.7405 (mp0) REVERT: A 578 TYR cc_start: 0.6536 (t80) cc_final: 0.6141 (t80) REVERT: A 633 LYS cc_start: 0.6375 (ptmm) cc_final: 0.5947 (tptp) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1244 time to fit residues: 10.7951 Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 = 0.4346 r_free = 0.4346 target = 0.184071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161742 restraints weight = 7640.299| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.33 r_work: 0.3967 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4969 Z= 0.164 Angle : 0.635 7.964 6838 Z= 0.331 Chirality : 0.046 0.385 768 Planarity : 0.006 0.053 785 Dihedral : 20.771 178.245 1004 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.10 % Allowed : 19.52 % Favored : 79.39 % 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: -0.29 (0.38), residues: 514 helix: 0.97 (0.34), residues: 221 sheet: -2.05 (0.63), residues: 56 loop : -0.77 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 262 TYR 0.023 0.003 TYR A 432 PHE 0.023 0.001 PHE A 102 TRP 0.045 0.003 TRP A 614 HIS 0.010 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 4969) covalent geometry : angle 0.63521 / 0.33 ( 6838) hydrogen bonds : bond 0.04156 / 2.79 ( 180) hydrogen bonds : angle 4.27943 / 2.94 ( 506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.159 Fit side-chains REVERT: A 74 GLU cc_start: 0.7223 (mp0) cc_final: 0.6986 (mp0) REVERT: A 96 ARG cc_start: 0.7291 (tmt-80) cc_final: 0.7033 (tpt90) REVERT: A 441 GLU cc_start: 0.7578 (mp0) cc_final: 0.7331 (mp0) REVERT: A 578 TYR cc_start: 0.6531 (t80) cc_final: 0.6127 (t80) REVERT: A 633 LYS cc_start: 0.6386 (ptmm) cc_final: 0.5960 (tptp) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1236 time to fit residues: 10.3867 Evaluate side-chains 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 = 0.4360 r_free = 0.4360 target = 0.185257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162989 restraints weight = 7649.721| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.33 r_work: 0.3980 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4969 Z= 0.145 Angle : 0.648 9.311 6838 Z= 0.338 Chirality : 0.045 0.382 768 Planarity : 0.006 0.052 785 Dihedral : 20.788 178.439 1004 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.10 % Allowed : 20.83 % Favored : 78.07 % 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 (0.38), residues: 514 helix: 1.06 (0.34), residues: 221 sheet: -2.05 (0.62), residues: 56 loop : -0.73 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 262 TYR 0.021 0.002 TYR A 432 PHE 0.021 0.001 PHE A 102 TRP 0.029 0.003 TRP A 614 HIS 0.009 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4969) covalent geometry : angle 0.64836 / 0.34 ( 6838) hydrogen bonds : bond 0.03918 / 2.62 ( 180) hydrogen bonds : angle 4.22141 / 2.91 ( 506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.162 Fit side-chains REVERT: A 74 GLU cc_start: 0.7227 (mp0) cc_final: 0.6976 (mp0) REVERT: A 96 ARG cc_start: 0.7267 (tmt-80) cc_final: 0.7013 (tpt90) REVERT: A 441 GLU cc_start: 0.7570 (mp0) cc_final: 0.7304 (mp0) REVERT: A 578 TYR cc_start: 0.6504 (t80) cc_final: 0.6096 (t80) REVERT: A 633 LYS cc_start: 0.6406 (ptmm) cc_final: 0.5960 (tptp) outliers start: 5 outliers final: 5 residues processed: 66 average time/residue: 0.1173 time to fit residues: 9.1875 Evaluate side-chains 66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 18 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 = 0.4349 r_free = 0.4349 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161766 restraints weight = 7664.419| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.42 r_work: 0.3954 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4969 Z= 0.173 Angle : 0.665 8.213 6838 Z= 0.346 Chirality : 0.046 0.387 768 Planarity : 0.006 0.069 785 Dihedral : 20.741 178.577 1004 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.10 % Allowed : 21.49 % Favored : 77.41 % 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: -0.30 (0.38), residues: 514 helix: 0.99 (0.34), residues: 222 sheet: -2.02 (0.65), residues: 56 loop : -0.82 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 262 TYR 0.021 0.003 TYR A 432 PHE 0.019 0.001 PHE A 102 TRP 0.051 0.003 TRP A 614 HIS 0.010 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 4969) covalent geometry : angle 0.66505 / 0.35 ( 6838) hydrogen bonds : bond 0.04136 / 2.76 ( 180) hydrogen bonds : angle 4.29994 / 2.94 ( 506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1403.02 seconds wall clock time: 24 minutes 49.76 seconds (1489.76 seconds total)