Starting phenix.real_space_refine on Tue Aug 4 13:31:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygr_72939/08_2026/9ygr_72939_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2085 2.51 5 N 554 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3312 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1581 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 189} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Time building chain proxies: 1.10, per 1000 atoms: 0.33 Number of scatterers: 3312 At special positions: 0 Unit cell: (64.4, 69, 92.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 647 8.00 N 554 7.00 C 2085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.62 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=1.29 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 0.32 Conformation dependent library (CDL) restraints added in 99.3 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 6.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.592A pdb=" N GLY A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.640A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA2, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.549A pdb=" N ASP A 578 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 506 removed outlier: 3.500A pdb=" N ARG A 517 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 522 through 523 removed outlier: 4.400A pdb=" N ASP A 523 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.642A pdb=" N LYS H 5 " --> pdb=" O ASN H 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS H 22 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR H 68 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.773A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL H 35A" --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR H 94 " --> pdb=" O HIS H 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS H 102 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.726A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1046 1.34 - 1.46: 830 1.46 - 1.58: 1488 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 3394 Sorted by residual: bond pdb=" N SER H 97 " pdb=" CA SER H 97 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.30e-02 5.92e+03 5.32e+00 bond pdb=" N GLY H 100B" pdb=" CA GLY H 100B" ideal model delta sigma weight residual 1.449 1.478 -0.029 1.45e-02 4.76e+03 3.98e+00 bond pdb=" CA SER H 97 " pdb=" CB SER H 97 " ideal model delta sigma weight residual 1.524 1.501 0.024 1.22e-02 6.72e+03 3.71e+00 bond pdb=" N ARG H 98 " pdb=" CA ARG H 98 " ideal model delta sigma weight residual 1.453 1.478 -0.026 1.44e-02 4.82e+03 3.16e+00 bond pdb=" C GLY H 100B" pdb=" O GLY H 100B" ideal model delta sigma weight residual 1.235 1.254 -0.020 1.35e-02 5.49e+03 2.14e+00 ... (remaining 3389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4350 1.46 - 2.92: 213 2.92 - 4.38: 37 4.38 - 5.83: 8 5.83 - 7.29: 7 Bond angle restraints: 4615 Sorted by residual: angle pdb=" CA TRP A 344 " pdb=" CB TRP A 344 " pdb=" CG TRP A 344 " ideal model delta sigma weight residual 113.60 120.47 -6.87 1.90e+00 2.77e-01 1.31e+01 angle pdb=" C ASN A 343 " pdb=" N TRP A 344 " pdb=" CA TRP A 344 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" CA CYS H 92 " pdb=" CB CYS H 92 " pdb=" SG CYS H 92 " ideal model delta sigma weight residual 114.40 121.69 -7.29 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C THR H 82A" pdb=" N ASN H 82B" pdb=" CA ASN H 82B" ideal model delta sigma weight residual 121.53 128.12 -6.59 2.25e+00 1.98e-01 8.57e+00 angle pdb=" C TYR L 49 " pdb=" N ALA L 50 " pdb=" CA ALA L 50 " ideal model delta sigma weight residual 123.05 127.49 -4.44 1.57e+00 4.06e-01 7.99e+00 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.16: 1845 11.16 - 22.31: 131 22.31 - 33.47: 44 33.47 - 44.63: 13 44.63 - 55.79: 5 Dihedral angle restraints: 2038 sinusoidal: 792 harmonic: 1246 Sorted by residual: dihedral pdb=" CA SER L 94 " pdb=" C SER L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ARG L 30 " pdb=" CB ARG L 30 " pdb=" CG ARG L 30 " pdb=" CD ARG L 30 " ideal model delta sinusoidal sigma weight residual -60.00 -115.79 55.79 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CA ASP A 400 " pdb=" CB ASP A 400 " pdb=" CG ASP A 400 " pdb=" OD1 ASP A 400 " ideal model delta sinusoidal sigma weight residual -30.00 -82.39 52.39 1 2.00e+01 2.50e-03 9.35e+00 ... (remaining 2035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 318 0.036 - 0.071: 125 0.071 - 0.107: 45 0.107 - 0.142: 17 0.142 - 0.178: 6 Chirality restraints: 511 Sorted by residual: chirality pdb=" CA TRP A 344 " pdb=" N TRP A 344 " pdb=" C TRP A 344 " pdb=" CB TRP A 344 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA SER L 94 " pdb=" N SER L 94 " pdb=" C SER L 94 " pdb=" CB SER L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 508 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 98 " 0.221 9.50e-02 1.11e+02 9.92e-02 6.05e+00 pdb=" NE ARG H 98 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG H 98 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG H 98 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 98 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 102 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C HIS H 102 " 0.038 2.00e-02 2.50e+03 pdb=" O HIS H 102 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP H 103 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 546 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 547 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " -0.025 5.00e-02 4.00e+02 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1014 2.83 - 3.35: 2778 3.35 - 3.87: 5354 3.87 - 4.38: 5869 4.38 - 4.90: 10208 Nonbonded interactions: 25223 Sorted by model distance: nonbonded pdb=" O LEU A 403 " pdb=" CD1 LEU A 403 " model vdw 2.315 3.460 nonbonded pdb=" O GLY A 407 " pdb=" OG SER A 411 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.360 3.040 nonbonded pdb=" OD2 ASP A 389 " pdb=" OH TYR A 414 " model vdw 2.378 3.040 nonbonded pdb=" N ASP A 478 " pdb=" OD1 ASP A 478 " model vdw 2.394 3.120 ... (remaining 25218 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.490 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.980 Find NCS groups from input model: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 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 : 0.017 0.742 3403 Z= 0.834 Angle : 1.138 54.258 4633 Z= 0.573 Chirality : 0.049 0.178 511 Planarity : 0.008 0.099 590 Dihedral : 9.477 55.786 1209 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.05 % Allowed : 8.38 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.40), residues: 416 helix: -2.36 (1.36), residues: 12 sheet: 0.45 (0.54), residues: 97 loop : -1.21 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 66 TYR 0.013 0.001 TYR L 49 PHE 0.014 0.002 PHE H 24 TRP 0.024 0.002 TRP A 344 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 ( 3394) covalent geometry : angle 0.75711 / 0.41 ( 4615) SS BOND : bond 0.31532 / 21.29 ( 9) SS BOND : angle 13.65264 / 8.80 ( 18) hydrogen bonds : bond 0.29845 / 19.62 ( 62) hydrogen bonds : angle 9.50240 / 6.08 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.078 Fit side-chains REVERT: A 393 ILE cc_start: 0.7993 (pt) cc_final: 0.7585 (mp) REVERT: L 37 GLN cc_start: 0.8149 (tt0) cc_final: 0.7788 (tm-30) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.0723 time to fit residues: 9.6793 Evaluate side-chains 71 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0870 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160611 restraints weight = 5416.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.164224 restraints weight = 3284.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166807 restraints weight = 2243.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.168671 restraints weight = 1664.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.169899 restraints weight = 1310.153| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3403 Z= 0.141 Angle : 0.621 7.125 4633 Z= 0.324 Chirality : 0.043 0.151 511 Planarity : 0.006 0.066 590 Dihedral : 4.641 39.930 463 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.57 % Allowed : 15.97 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.40), residues: 416 helix: -4.48 (0.76), residues: 6 sheet: 0.50 (0.51), residues: 103 loop : -1.11 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 58 TYR 0.040 0.003 TYR L 49 PHE 0.017 0.002 PHE L 98 TRP 0.017 0.001 TRP A 344 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 3394) covalent geometry : angle 0.61941 / 0.32 ( 4615) SS BOND : bond 0.00317 / 0.20 ( 9) SS BOND : angle 0.93184 / 0.55 ( 18) hydrogen bonds : bond 0.03998 / 2.42 ( 62) hydrogen bonds : angle 6.57483 / 4.28 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.079 Fit side-chains REVERT: A 393 ILE cc_start: 0.7839 (pt) cc_final: 0.7455 (mp) REVERT: H 10 MET cc_start: 0.4858 (tpp) cc_final: 0.4505 (ttm) REVERT: H 51 ILE cc_start: 0.7397 (tp) cc_final: 0.7055 (tt) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.0377 time to fit residues: 3.8550 Evaluate side-chains 71 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159328 restraints weight = 5345.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162794 restraints weight = 3314.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165110 restraints weight = 2278.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.166976 restraints weight = 1718.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168158 restraints weight = 1368.742| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3403 Z= 0.128 Angle : 0.584 6.030 4633 Z= 0.301 Chirality : 0.042 0.148 511 Planarity : 0.005 0.059 590 Dihedral : 4.615 41.597 461 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.66 % Allowed : 17.54 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.39), residues: 416 helix: -4.56 (0.71), residues: 6 sheet: 0.42 (0.51), residues: 103 loop : -1.20 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.023 0.002 TYR L 49 PHE 0.016 0.001 PHE L 98 TRP 0.028 0.002 TRP L 35 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 3394) covalent geometry : angle 0.58409 / 0.30 ( 4615) SS BOND : bond 0.00196 / 0.13 ( 9) SS BOND : angle 0.68084 / 0.39 ( 18) hydrogen bonds : bond 0.03691 / 2.30 ( 62) hydrogen bonds : angle 6.30212 / 4.12 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.073 Fit side-chains REVERT: A 393 ILE cc_start: 0.7751 (pt) cc_final: 0.7416 (mp) REVERT: A 402 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6866 (mm-40) REVERT: H 10 MET cc_start: 0.4878 (tpp) cc_final: 0.4534 (ttp) REVERT: H 51 ILE cc_start: 0.7453 (tp) cc_final: 0.7067 (tt) REVERT: L 55 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7357 (tm-30) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 0.0259 time to fit residues: 2.7520 Evaluate side-chains 70 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4125 r_free = 0.4125 target = 0.176634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159888 restraints weight = 5383.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162568 restraints weight = 3582.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164579 restraints weight = 2617.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166012 restraints weight = 2042.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166941 restraints weight = 1677.553| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3403 Z= 0.123 Angle : 0.571 5.317 4633 Z= 0.292 Chirality : 0.043 0.165 511 Planarity : 0.005 0.052 590 Dihedral : 4.509 40.655 461 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.45 % Allowed : 16.23 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.39), residues: 416 helix: -3.78 (1.01), residues: 12 sheet: 0.42 (0.51), residues: 103 loop : -1.23 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.017 0.002 TYR L 71 PHE 0.018 0.001 PHE L 98 TRP 0.030 0.002 TRP L 35 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 3394) covalent geometry : angle 0.57078 / 0.29 ( 4615) SS BOND : bond 0.00345 / 0.24 ( 9) SS BOND : angle 0.53681 / 0.29 ( 18) hydrogen bonds : bond 0.03229 / 2.01 ( 62) hydrogen bonds : angle 5.96492 / 3.98 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.124 Fit side-chains REVERT: A 393 ILE cc_start: 0.7735 (pt) cc_final: 0.7420 (mp) REVERT: A 402 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6923 (mm-40) REVERT: H 51 ILE cc_start: 0.7515 (tp) cc_final: 0.7138 (tt) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.0402 time to fit residues: 4.7687 Evaluate side-chains 79 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN A 545 HIS L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.171397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152350 restraints weight = 5343.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155557 restraints weight = 3429.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.157870 restraints weight = 2431.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159560 restraints weight = 1865.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160354 restraints weight = 1511.441| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3403 Z= 0.182 Angle : 0.647 6.387 4633 Z= 0.332 Chirality : 0.045 0.156 511 Planarity : 0.005 0.052 590 Dihedral : 4.795 39.701 461 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.19 % Allowed : 17.02 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.40), residues: 416 helix: -4.03 (0.83), residues: 13 sheet: 0.18 (0.52), residues: 107 loop : -1.23 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.024 0.003 TYR L 49 PHE 0.023 0.002 PHE L 98 TRP 0.029 0.002 TRP L 35 HIS 0.009 0.002 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 3394) covalent geometry : angle 0.64031 / 0.33 ( 4615) SS BOND : bond 0.00188 / 0.12 ( 9) SS BOND : angle 1.60741 / 0.90 ( 18) hydrogen bonds : bond 0.03096 / 1.89 ( 62) hydrogen bonds : angle 5.74398 / 3.83 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.165 Fit side-chains REVERT: A 393 ILE cc_start: 0.7851 (pt) cc_final: 0.7546 (mp) REVERT: H 51 ILE cc_start: 0.7685 (tp) cc_final: 0.7309 (tt) outliers start: 16 outliers final: 15 residues processed: 84 average time/residue: 0.0339 time to fit residues: 3.9927 Evaluate side-chains 86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4063 r_free = 0.4063 target = 0.170680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150930 restraints weight = 5447.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154237 restraints weight = 3490.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156691 restraints weight = 2475.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158333 restraints weight = 1903.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159666 restraints weight = 1549.430| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3403 Z= 0.153 Angle : 0.636 6.799 4633 Z= 0.323 Chirality : 0.044 0.141 511 Planarity : 0.005 0.063 590 Dihedral : 4.780 39.371 461 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.97 % Allowed : 17.54 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.40), residues: 416 helix: -4.19 (0.73), residues: 13 sheet: 0.17 (0.56), residues: 99 loop : -1.27 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.022 0.002 TYR A 462 PHE 0.022 0.001 PHE L 98 TRP 0.018 0.002 TRP L 35 HIS 0.005 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 3394) covalent geometry : angle 0.63189 / 0.32 ( 4615) SS BOND : bond 0.00196 / 0.13 ( 9) SS BOND : angle 1.36957 / 0.79 ( 18) hydrogen bonds : bond 0.02913 / 1.83 ( 62) hydrogen bonds : angle 5.64940 / 3.74 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.129 Fit side-chains REVERT: A 393 ILE cc_start: 0.7879 (pt) cc_final: 0.7517 (mp) REVERT: A 402 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6877 (mm-40) REVERT: H 51 ILE cc_start: 0.7567 (tp) cc_final: 0.7194 (tt) outliers start: 19 outliers final: 18 residues processed: 88 average time/residue: 0.0421 time to fit residues: 5.0047 Evaluate side-chains 90 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4073 r_free = 0.4073 target = 0.172300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153189 restraints weight = 5380.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156323 restraints weight = 3493.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158566 restraints weight = 2489.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.160099 restraints weight = 1922.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161368 restraints weight = 1573.907| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3403 Z= 0.147 Angle : 0.640 7.338 4633 Z= 0.324 Chirality : 0.044 0.168 511 Planarity : 0.005 0.058 590 Dihedral : 4.769 38.454 461 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.97 % Allowed : 18.85 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.40), residues: 416 helix: -4.28 (0.65), residues: 13 sheet: 0.17 (0.57), residues: 99 loop : -1.30 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.026 0.002 TYR L 49 PHE 0.026 0.001 PHE L 98 TRP 0.013 0.002 TRP L 35 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3394) covalent geometry : angle 0.63645 / 0.32 ( 4615) SS BOND : bond 0.00179 / 0.12 ( 9) SS BOND : angle 1.23899 / 0.67 ( 18) hydrogen bonds : bond 0.02884 / 1.81 ( 62) hydrogen bonds : angle 5.64425 / 3.72 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.076 Fit side-chains REVERT: A 393 ILE cc_start: 0.7847 (pt) cc_final: 0.7565 (mp) REVERT: H 51 ILE cc_start: 0.7718 (tp) cc_final: 0.7202 (tt) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.0251 time to fit residues: 3.0971 Evaluate side-chains 89 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4062 r_free = 0.4062 target = 0.171340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151418 restraints weight = 5398.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.154601 restraints weight = 3507.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156926 restraints weight = 2508.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158587 restraints weight = 1939.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.159728 restraints weight = 1582.778| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3403 Z= 0.181 Angle : 0.696 8.331 4633 Z= 0.351 Chirality : 0.045 0.150 511 Planarity : 0.005 0.062 590 Dihedral : 4.953 36.280 461 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.50 % Allowed : 20.16 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.41), residues: 416 helix: -5.04 (0.61), residues: 6 sheet: 0.08 (0.56), residues: 99 loop : -1.30 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.022 0.002 TYR A 462 PHE 0.024 0.001 PHE L 98 TRP 0.013 0.002 TRP L 35 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 3394) covalent geometry : angle 0.69212 / 0.35 ( 4615) SS BOND : bond 0.00184 / 0.11 ( 9) SS BOND : angle 1.31404 / 0.73 ( 18) hydrogen bonds : bond 0.02884 / 1.80 ( 62) hydrogen bonds : angle 5.66490 / 3.68 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.077 Fit side-chains REVERT: H 51 ILE cc_start: 0.7782 (tp) cc_final: 0.7221 (tt) REVERT: L 49 TYR cc_start: 0.8302 (p90) cc_final: 0.7772 (p90) REVERT: L 97 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7729 (t) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.0291 time to fit residues: 3.3893 Evaluate side-chains 86 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.0050 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4042 r_free = 0.4042 target = 0.169858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150016 restraints weight = 5341.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153147 restraints weight = 3459.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155461 restraints weight = 2490.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157188 restraints weight = 1925.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158461 restraints weight = 1549.852| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3403 Z= 0.176 Angle : 0.698 8.877 4633 Z= 0.350 Chirality : 0.044 0.142 511 Planarity : 0.005 0.054 590 Dihedral : 5.060 35.209 461 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.45 % Allowed : 20.94 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.41), residues: 416 helix: -5.04 (0.63), residues: 6 sheet: 0.19 (0.54), residues: 103 loop : -1.30 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 66 TYR 0.020 0.002 TYR A 462 PHE 0.018 0.001 PHE L 98 TRP 0.013 0.002 TRP L 35 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 3394) covalent geometry : angle 0.69351 / 0.35 ( 4615) SS BOND : bond 0.00298 / 0.19 ( 9) SS BOND : angle 1.47292 / 0.88 ( 18) hydrogen bonds : bond 0.02890 / 1.80 ( 62) hydrogen bonds : angle 5.70007 / 3.67 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.154 Fit side-chains REVERT: H 51 ILE cc_start: 0.7660 (tp) cc_final: 0.7069 (tt) REVERT: H 100 ILE cc_start: 0.8018 (mm) cc_final: 0.7812 (mm) REVERT: L 90 GLN cc_start: 0.7758 (pp30) cc_final: 0.7341 (pp30) outliers start: 17 outliers final: 16 residues processed: 86 average time/residue: 0.0469 time to fit residues: 5.3131 Evaluate side-chains 85 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 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 = 0.4076 r_free = 0.4076 target = 0.173723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154994 restraints weight = 5261.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158095 restraints weight = 3307.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160207 restraints weight = 2329.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162050 restraints weight = 1784.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.163148 restraints weight = 1430.696| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3403 Z= 0.134 Angle : 0.687 8.281 4633 Z= 0.341 Chirality : 0.044 0.141 511 Planarity : 0.006 0.069 590 Dihedral : 4.990 28.373 461 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.93 % Allowed : 21.99 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.41), residues: 416 helix: -5.00 (0.64), residues: 6 sheet: 0.36 (0.53), residues: 113 loop : -1.30 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.030 0.002 TYR L 49 PHE 0.022 0.002 PHE L 98 TRP 0.014 0.002 TRP L 35 HIS 0.002 0.001 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3394) covalent geometry : angle 0.68315 / 0.34 ( 4615) SS BOND : bond 0.00150 / 0.10 ( 9) SS BOND : angle 1.29280 / 0.79 ( 18) hydrogen bonds : bond 0.02784 / 1.77 ( 62) hydrogen bonds : angle 5.58898 / 3.63 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.124 Fit side-chains REVERT: A 402 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6565 (mm-40) REVERT: H 51 ILE cc_start: 0.7558 (tp) cc_final: 0.6980 (tt) REVERT: H 100 ILE cc_start: 0.7904 (mm) cc_final: 0.7660 (mm) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.0442 time to fit residues: 4.9788 Evaluate side-chains 80 residues out of total 386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.0010 chunk 37 optimal weight: 0.0870 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152919 restraints weight = 5368.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156059 restraints weight = 3437.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158296 restraints weight = 2443.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.159704 restraints weight = 1882.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161064 restraints weight = 1549.142| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3403 Z= 0.131 Angle : 0.734 16.738 4633 Z= 0.351 Chirality : 0.043 0.139 511 Planarity : 0.005 0.049 590 Dihedral : 4.760 23.137 460 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.66 % Allowed : 22.77 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.42), residues: 416 helix: -4.95 (0.64), residues: 6 sheet: 0.44 (0.52), residues: 113 loop : -1.24 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 398 TYR 0.018 0.002 TYR A 462 PHE 0.020 0.001 PHE L 98 TRP 0.013 0.002 TRP A 344 HIS 0.002 0.000 HIS A 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 3394) covalent geometry : angle 0.73170 / 0.35 ( 4615) SS BOND : bond 0.00169 / 0.11 ( 9) SS BOND : angle 1.12872 / 0.67 ( 18) hydrogen bonds : bond 0.02950 / 1.80 ( 62) hydrogen bonds : angle 5.70633 / 3.61 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 849.01 seconds wall clock time: 15 minutes 20.14 seconds (920.14 seconds total)