Starting phenix.real_space_refine on Sun Apr 27 06:27:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_37789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_37789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_37789.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_37789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrt_37789/04_2025/8wrt_37789.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.23, per 1000 atoms: 0.88 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: 1.38 Conformation dependent library (CDL) restraints added in 534.3 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: 1.50 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: 1.41 Time building geometry restraints manager: 1.64 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: 6610 1.90 - 3.79: 194 3.79 - 5.69: 28 5.69 - 7.59: 4 7.59 - 9.49: 2 Bond angle restraints: 6838 Sorted by residual: 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=" 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=" C ASN A 195 " pdb=" N PRO A 196 " pdb=" CA PRO A 196 " ideal model delta sigma weight residual 119.84 115.57 4.27 1.25e+00 6.40e-01 1.17e+01 angle pdb=" CA PRO A 239 " pdb=" N PRO A 239 " pdb=" CD PRO A 239 " ideal model delta sigma weight residual 112.00 107.23 4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" N PRO A 192 " pdb=" CA PRO A 192 " pdb=" C PRO A 192 " ideal model delta sigma weight residual 111.21 116.23 -5.02 1.59e+00 3.96e-01 9.96e+00 ... (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: 650 0.060 - 0.119: 102 0.119 - 0.179: 12 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: 2.810 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 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= 0.195 Angle : 0.744 9.487 6838 Z= 0.450 Chirality : 0.046 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP A 626 HIS 0.004 0.001 HIS A 632 PHE 0.015 0.002 PHE A 335 TYR 0.011 0.001 TYR A 578 ARG 0.006 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.25320 ( 180) hydrogen bonds : angle 8.40816 ( 506) covalent geometry : bond 0.00318 ( 4969) covalent geometry : angle 0.74406 ( 6838) *********************** 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 : 0.444 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: 0.6108 (m-30) REVERT: A 371 LYS cc_start: 0.6433 (mppt) cc_final: 0.6007 (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: 0.2893 time to fit residues: 25.0134 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 : 0.497 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.0670 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.183380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161123 restraints weight = 7622.188| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.41 r_work: 0.3950 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4969 Z= 0.172 Angle : 0.652 6.379 6838 Z= 0.338 Chirality : 0.044 0.206 768 Planarity : 0.007 0.089 785 Dihedral : 20.699 177.265 1006 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.10 % Allowed : 9.87 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.37), residues: 514 helix: 0.64 (0.34), residues: 212 sheet: -2.32 (0.66), residues: 51 loop : -0.58 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.009 0.002 HIS A 641 PHE 0.023 0.002 PHE A 335 TYR 0.027 0.003 TYR A 123 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 180) hydrogen bonds : angle 4.68623 ( 506) covalent geometry : bond 0.00370 ( 4969) covalent geometry : angle 0.65238 ( 6838) *********************** 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 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7342 (tmt-80) cc_final: 0.6978 (tpt170) REVERT: A 166 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6337 (tm-30) REVERT: A 308 ASP cc_start: 0.6986 (m-30) cc_final: 0.6619 (m-30) REVERT: A 444 LYS cc_start: 0.8313 (tmmt) cc_final: 0.8013 (tmmt) REVERT: A 573 ARG cc_start: 0.6671 (mpp80) cc_final: 0.6447 (mpp80) REVERT: A 578 TYR cc_start: 0.6367 (t80) cc_final: 0.6004 (t80) REVERT: A 633 LYS cc_start: 0.6374 (ptmm) cc_final: 0.5930 (tptp) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.3097 time to fit residues: 24.6223 Evaluate side-chains 65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 490 SER 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 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.183267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161143 restraints weight = 7668.639| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.34 r_work: 0.3954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4969 Z= 0.157 Angle : 0.592 6.376 6838 Z= 0.308 Chirality : 0.043 0.204 768 Planarity : 0.006 0.068 785 Dihedral : 20.749 177.255 1004 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.66 % Allowed : 15.35 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.37), residues: 514 helix: 0.82 (0.33), residues: 224 sheet: -2.04 (0.67), residues: 51 loop : -0.59 (0.43), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.011 0.002 HIS A 641 PHE 0.020 0.001 PHE A 102 TYR 0.017 0.002 TYR A 432 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 180) hydrogen bonds : angle 4.35632 ( 506) covalent geometry : bond 0.00344 ( 4969) covalent geometry : angle 0.59230 ( 6838) *********************** 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 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7335 (tmt-80) cc_final: 0.7046 (tpt90) REVERT: A 578 TYR cc_start: 0.6476 (t80) cc_final: 0.6061 (t80) REVERT: A 633 LYS cc_start: 0.6384 (ptmm) cc_final: 0.5951 (tptp) outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.2743 time to fit residues: 22.3981 Evaluate side-chains 68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 490 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** 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 = 0.4372 r_free = 0.4372 target = 0.186189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164094 restraints weight = 7698.337| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.33 r_work: 0.3994 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2869 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= 0.123 Angle : 0.547 5.497 6838 Z= 0.283 Chirality : 0.041 0.201 768 Planarity : 0.006 0.054 785 Dihedral : 20.642 177.241 1004 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.54 % Allowed : 16.23 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.38), residues: 514 helix: 1.15 (0.34), residues: 228 sheet: -1.95 (0.63), residues: 56 loop : -0.42 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 112 HIS 0.008 0.001 HIS A 641 PHE 0.016 0.001 PHE A 102 TYR 0.016 0.002 TYR A 432 ARG 0.008 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 180) hydrogen bonds : angle 4.00052 ( 506) covalent geometry : bond 0.00271 ( 4969) covalent geometry : angle 0.54708 ( 6838) *********************** 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 70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7291 (tmt-80) cc_final: 0.6997 (tpt90) REVERT: A 578 TYR cc_start: 0.6459 (t80) cc_final: 0.6052 (t80) REVERT: A 633 LYS cc_start: 0.6420 (ptmm) cc_final: 0.5970 (tptp) outliers start: 7 outliers final: 3 residues processed: 69 average time/residue: 0.3286 time to fit residues: 26.6821 Evaluate side-chains 68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 464 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.0020 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.184906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.162764 restraints weight = 7714.634| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.34 r_work: 0.3967 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4969 Z= 0.150 Angle : 0.583 6.703 6838 Z= 0.301 Chirality : 0.042 0.205 768 Planarity : 0.006 0.052 785 Dihedral : 20.662 176.998 1004 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.88 % Allowed : 18.42 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.38), residues: 514 helix: 1.21 (0.34), residues: 224 sheet: -1.94 (0.63), residues: 56 loop : -0.43 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.008 0.001 HIS A 641 PHE 0.030 0.002 PHE A 102 TYR 0.018 0.002 TYR A 123 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 180) hydrogen bonds : angle 4.01599 ( 506) covalent geometry : bond 0.00336 ( 4969) covalent geometry : angle 0.58302 ( 6838) *********************** 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: 4 poor density : 67 time to evaluate : 0.520 Fit side-chains REVERT: A 441 GLU cc_start: 0.7595 (mp0) cc_final: 0.7379 (mp0) REVERT: A 578 TYR cc_start: 0.6515 (t80) cc_final: 0.6075 (t80) REVERT: A 633 LYS cc_start: 0.6451 (ptmm) cc_final: 0.6004 (tptp) outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.2781 time to fit residues: 23.3909 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 : 0.486 ------------------------------------------------------------------------------- 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 490 SER Chi-restraints excluded: chain A residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.185467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.163593 restraints weight = 7740.061| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.33 r_work: 0.3987 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4969 Z= 0.136 Angle : 0.576 7.229 6838 Z= 0.296 Chirality : 0.041 0.203 768 Planarity : 0.005 0.051 785 Dihedral : 20.628 176.765 1004 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.41 % Allowed : 18.42 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.38), residues: 514 helix: 1.33 (0.34), residues: 228 sheet: -1.92 (0.63), residues: 56 loop : -0.43 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 614 HIS 0.008 0.001 HIS A 641 PHE 0.021 0.001 PHE A 102 TYR 0.018 0.002 TYR A 123 ARG 0.008 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 180) hydrogen bonds : angle 3.88387 ( 506) covalent geometry : bond 0.00303 ( 4969) covalent geometry : angle 0.57631 ( 6838) *********************** 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 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7210 (mp0) cc_final: 0.6507 (mp0) REVERT: A 441 GLU cc_start: 0.7608 (mp0) cc_final: 0.7407 (mp0) REVERT: A 488 MET cc_start: 0.3874 (tpp) cc_final: 0.3382 (ptt) REVERT: A 633 LYS cc_start: 0.6452 (ptmm) cc_final: 0.5989 (tptp) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.2754 time to fit residues: 24.4288 Evaluate side-chains 75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 464 GLN 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 7 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.4322 r_free = 0.4322 target = 0.181962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.160420 restraints weight = 7602.953| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.26 r_work: 0.3940 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4969 Z= 0.186 Angle : 0.642 7.850 6838 Z= 0.333 Chirality : 0.043 0.211 768 Planarity : 0.006 0.053 785 Dihedral : 20.635 176.988 1004 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.41 % Allowed : 18.86 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.38), residues: 514 helix: 1.22 (0.34), residues: 225 sheet: -1.92 (0.66), residues: 56 loop : -0.59 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 614 HIS 0.012 0.002 HIS A 641 PHE 0.025 0.002 PHE A 102 TYR 0.023 0.003 TYR A 123 ARG 0.009 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 180) hydrogen bonds : angle 4.10509 ( 506) covalent geometry : bond 0.00411 ( 4969) covalent geometry : angle 0.64235 ( 6838) *********************** 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 75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 238 ILE cc_start: 0.7923 (mp) cc_final: 0.7720 (mp) REVERT: A 633 LYS cc_start: 0.6449 (ptmm) cc_final: 0.6022 (tptp) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.2733 time to fit residues: 23.8462 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 464 GLN 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 7 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.183359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161062 restraints weight = 7742.994| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.44 r_work: 0.3937 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4969 Z= 0.170 Angle : 0.630 7.245 6838 Z= 0.327 Chirality : 0.043 0.209 768 Planarity : 0.006 0.056 785 Dihedral : 20.601 176.492 1004 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.75 % Allowed : 20.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.38), residues: 514 helix: 1.08 (0.34), residues: 227 sheet: -2.03 (0.66), residues: 56 loop : -0.57 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 614 HIS 0.010 0.002 HIS A 641 PHE 0.019 0.001 PHE A 102 TYR 0.029 0.003 TYR A 578 ARG 0.009 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 180) hydrogen bonds : angle 4.09217 ( 506) covalent geometry : bond 0.00380 ( 4969) covalent geometry : angle 0.62986 ( 6838) *********************** 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 71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7322 (tmt-80) cc_final: 0.7087 (tpt90) REVERT: A 238 ILE cc_start: 0.7958 (mp) cc_final: 0.7756 (mp) REVERT: A 434 ARG cc_start: 0.7478 (ttt-90) cc_final: 0.7269 (ttt-90) REVERT: A 633 LYS cc_start: 0.6471 (ptmm) cc_final: 0.6022 (tptp) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.3287 time to fit residues: 27.5537 Evaluate side-chains 72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 464 GLN 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 15 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.183168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160868 restraints weight = 7621.658| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.41 r_work: 0.3933 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4969 Z= 0.184 Angle : 0.648 7.828 6838 Z= 0.337 Chirality : 0.043 0.211 768 Planarity : 0.006 0.056 785 Dihedral : 20.561 176.611 1004 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.75 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.38), residues: 514 helix: 1.13 (0.34), residues: 223 sheet: -2.05 (0.68), residues: 56 loop : -0.71 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 436 HIS 0.012 0.002 HIS A 641 PHE 0.018 0.001 PHE A 102 TYR 0.029 0.003 TYR A 578 ARG 0.010 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 180) hydrogen bonds : angle 4.15295 ( 506) covalent geometry : bond 0.00411 ( 4969) covalent geometry : angle 0.64768 ( 6838) *********************** 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 76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.777 Fit side-chains REVERT: A 74 GLU cc_start: 0.7192 (mp0) cc_final: 0.6736 (mm-30) REVERT: A 238 ILE cc_start: 0.7961 (mp) cc_final: 0.7759 (mp) REVERT: A 434 ARG cc_start: 0.7442 (ttt-90) cc_final: 0.7221 (ttt-90) REVERT: A 468 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 633 LYS cc_start: 0.6488 (ptmm) cc_final: 0.6043 (tptp) outliers start: 8 outliers final: 8 residues processed: 73 average time/residue: 0.3230 time to fit residues: 28.9106 Evaluate side-chains 77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 TRP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 443 ILE 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 42 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** 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 = 0.4351 r_free = 0.4351 target = 0.184347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162414 restraints weight = 7732.805| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.35 r_work: 0.3962 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4969 Z= 0.150 Angle : 0.615 7.587 6838 Z= 0.319 Chirality : 0.042 0.205 768 Planarity : 0.005 0.055 785 Dihedral : 20.550 176.750 1004 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.38), residues: 514 helix: 1.12 (0.34), residues: 232 sheet: -2.14 (0.65), residues: 56 loop : -0.69 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 436 HIS 0.009 0.001 HIS A 641 PHE 0.017 0.001 PHE A 102 TYR 0.028 0.003 TYR A 578 ARG 0.009 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 180) hydrogen bonds : angle 4.03602 ( 506) covalent geometry : bond 0.00337 ( 4969) covalent geometry : angle 0.61528 ( 6838) ********************** 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 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.510 Fit side-chains REVERT: A 96 ARG cc_start: 0.7307 (tmt-80) cc_final: 0.6936 (tpt90) REVERT: A 434 ARG cc_start: 0.7451 (ttt-90) cc_final: 0.7223 (ttt-90) REVERT: A 633 LYS cc_start: 0.6491 (ptmm) cc_final: 0.6032 (tptp) outliers start: 7 outliers final: 7 residues processed: 68 average time/residue: 0.2628 time to fit residues: 21.4124 Evaluate side-chains 69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 TRP 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: 0.0970 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 28 optimal weight: 0.0770 chunk 33 optimal weight: 0.4980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A 472 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.188473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166832 restraints weight = 7714.719| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.38 r_work: 0.4016 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4969 Z= 0.112 Angle : 0.576 7.324 6838 Z= 0.298 Chirality : 0.041 0.191 768 Planarity : 0.005 0.053 785 Dihedral : 20.394 177.066 1004 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.32 % Allowed : 21.05 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.39), residues: 514 helix: 1.45 (0.35), residues: 230 sheet: -2.13 (0.63), residues: 56 loop : -0.57 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 436 HIS 0.005 0.001 HIS A 641 PHE 0.014 0.001 PHE A 102 TYR 0.024 0.002 TYR A 578 ARG 0.010 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 180) hydrogen bonds : angle 3.74819 ( 506) covalent geometry : bond 0.00254 ( 4969) covalent geometry : angle 0.57553 ( 6838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.74 seconds wall clock time: 53 minutes 49.55 seconds (3229.55 seconds total)