Starting phenix.real_space_refine on Wed Jul 1 23:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6t_62135/07_2026/9k6t_62135.cif" } resolution = 2.8 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 2520 2.51 5 N 758 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3332 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 25, 'TRANS': 395} Chain breaks: 2 Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "C" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 448 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.20, per 1000 atoms: 0.28 Number of scatterers: 4222 At special positions: 0 Unit cell: (67.26, 78.66, 98.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 42 15.00 Mg 1 11.99 O 882 8.00 N 758 7.00 C 2520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 133.9 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 3 sheets defined 33.0% alpha, 13.8% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.361A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.765A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 554' Processing helix chain 'A' and resid 556 through 571 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 675 through 692 removed outlier: 3.590A pdb=" N VAL A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 800 through 817 Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.785A pdb=" N PHE A 666 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 707 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG A 668 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 598 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.910A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 452 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 521 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 454 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 518 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL A 547 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 520 " --> pdb=" O VAL A 547 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 591 1.32 - 1.44: 1403 1.44 - 1.56: 2296 1.56 - 1.69: 84 1.69 - 1.81: 27 Bond restraints: 4401 Sorted by residual: bond pdb=" CG PRO A 700 " pdb=" CD PRO A 700 " ideal model delta sigma weight residual 1.503 1.338 0.165 3.40e-02 8.65e+02 2.36e+01 bond pdb=" CA LYS A 844 " pdb=" C LYS A 844 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" N LEU A 817 " pdb=" CA LEU A 817 " ideal model delta sigma weight residual 1.463 1.418 0.045 1.31e-02 5.83e+03 1.17e+01 bond pdb=" CA ALA A 841 " pdb=" C ALA A 841 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.37e+00 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 5919 2.81 - 5.62: 192 5.62 - 8.43: 43 8.43 - 11.23: 6 11.23 - 14.04: 3 Bond angle restraints: 6163 Sorted by residual: angle pdb=" N PRO A 700 " pdb=" CD PRO A 700 " pdb=" CG PRO A 700 " ideal model delta sigma weight residual 103.20 89.16 14.04 1.50e+00 4.44e-01 8.76e+01 angle pdb=" N LYS A 844 " pdb=" CA LYS A 844 " pdb=" C LYS A 844 " ideal model delta sigma weight residual 113.97 102.38 11.59 1.28e+00 6.10e-01 8.20e+01 angle pdb=" CA PRO A 700 " pdb=" N PRO A 700 " pdb=" CD PRO A 700 " ideal model delta sigma weight residual 112.00 102.54 9.46 1.40e+00 5.10e-01 4.57e+01 angle pdb=" CA PRO A 700 " pdb=" CB PRO A 700 " pdb=" CG PRO A 700 " ideal model delta sigma weight residual 104.50 93.11 11.39 1.90e+00 2.77e-01 3.59e+01 angle pdb=" N LEU A 768 " pdb=" CA LEU A 768 " pdb=" C LEU A 768 " ideal model delta sigma weight residual 113.55 106.31 7.24 1.26e+00 6.30e-01 3.30e+01 ... (remaining 6158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 2461 35.84 - 71.69: 206 71.69 - 107.53: 20 107.53 - 143.37: 1 143.37 - 179.22: 3 Dihedral angle restraints: 2691 sinusoidal: 1469 harmonic: 1222 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual -128.00 46.85 -174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C B 14 " pdb=" C1' C B 14 " pdb=" N1 C B 14 " pdb=" C2 C B 14 " ideal model delta sinusoidal sigma weight residual -160.00 -75.27 -84.73 1 1.50e+01 4.44e-03 3.87e+01 dihedral pdb=" O4' C C 6 " pdb=" C2' C C 6 " pdb=" C1' C C 6 " pdb=" C3' C C 6 " ideal model delta sinusoidal sigma weight residual 25.00 -15.05 40.05 1 8.00e+00 1.56e-02 3.52e+01 ... (remaining 2688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 632 0.111 - 0.222: 69 0.222 - 0.332: 2 0.332 - 0.443: 11 0.443 - 0.554: 13 Chirality restraints: 727 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" P U B 13 " pdb=" OP1 U B 13 " pdb=" OP2 U B 13 " pdb=" O5' U B 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" P A C 5 " pdb=" OP1 A C 5 " pdb=" OP2 A C 5 " pdb=" O5' A C 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.00e+00 ... (remaining 724 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 761 " -0.511 9.50e-02 1.11e+02 2.29e-01 3.21e+01 pdb=" NE ARG A 761 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 761 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 761 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 761 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 816 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C HIS A 816 " -0.081 2.00e-02 2.50e+03 pdb=" O HIS A 816 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU A 817 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 699 " 0.075 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO A 700 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " 0.057 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 397 2.74 - 3.28: 3931 3.28 - 3.82: 7823 3.82 - 4.36: 8879 4.36 - 4.90: 14376 Nonbonded interactions: 35406 Sorted by model distance: nonbonded pdb=" O GLN A 785 " pdb=" OG1 THR A 789 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 752 " pdb=" O VAL A 797 " model vdw 2.217 3.040 nonbonded pdb=" OE1 GLN A 652 " pdb=" OG SER A 656 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 632 " pdb=" O GLN A 636 " model vdw 2.378 3.120 nonbonded pdb=" O SER A 752 " pdb=" OG SER A 752 " model vdw 2.380 3.040 ... (remaining 35401 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: 0.340 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.165 4401 Z= 0.430 Angle : 1.222 14.042 6163 Z= 0.728 Chirality : 0.105 0.554 727 Planarity : 0.013 0.229 639 Dihedral : 23.560 179.217 1903 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.06 % Favored : 94.22 % Rotamer: Outliers : 3.32 % Allowed : 26.04 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.39), residues: 415 helix: -0.99 (0.40), residues: 140 sheet: -1.62 (0.50), residues: 85 loop : -1.10 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 854 TYR 0.031 0.002 TYR A 805 PHE 0.024 0.003 PHE A 653 TRP 0.013 0.002 TRP A 435 HIS 0.011 0.002 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.43 ( 4401) covalent geometry : angle 1.22207 / 0.73 ( 6163) hydrogen bonds : bond 0.15165 / 9.97 ( 154) hydrogen bonds : angle 7.82008 / 5.72 ( 416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.097 Fit side-chains REVERT: A 761 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.4060 (mmt-90) REVERT: A 844 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7812 (mtmt) outliers start: 12 outliers final: 3 residues processed: 54 average time/residue: 0.4932 time to fit residues: 27.4080 Evaluate side-chains 41 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 ARG Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 844 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 588 GLN ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN A 807 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.252611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.198961 restraints weight = 4817.677| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.50 r_work: 0.4233 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4401 Z= 0.160 Angle : 0.692 9.995 6163 Z= 0.381 Chirality : 0.049 0.238 727 Planarity : 0.006 0.056 639 Dihedral : 23.930 178.508 1109 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.26 % Allowed : 26.04 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.40), residues: 415 helix: -0.06 (0.43), residues: 141 sheet: -1.67 (0.49), residues: 85 loop : -0.92 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 710 TYR 0.017 0.002 TYR A 765 PHE 0.014 0.001 PHE A 653 TRP 0.011 0.002 TRP A 769 HIS 0.011 0.002 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 4401) covalent geometry : angle 0.69171 / 0.38 ( 6163) hydrogen bonds : bond 0.05263 / 3.55 ( 154) hydrogen bonds : angle 5.86853 / 4.05 ( 416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.132 Fit side-chains REVERT: A 447 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5784 (tm-30) REVERT: A 549 MET cc_start: 0.5361 (tpp) cc_final: 0.4309 (ptm) REVERT: A 804 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6240 (m-80) outliers start: 19 outliers final: 8 residues processed: 59 average time/residue: 0.2858 time to fit residues: 17.8282 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 807 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.252489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198163 restraints weight = 4762.831| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.51 r_work: 0.4211 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4401 Z= 0.151 Angle : 0.655 9.490 6163 Z= 0.352 Chirality : 0.048 0.216 727 Planarity : 0.005 0.047 639 Dihedral : 23.705 175.296 1101 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.26 % Allowed : 30.75 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.00 (0.41), residues: 415 helix: 0.24 (0.43), residues: 141 sheet: -1.57 (0.48), residues: 89 loop : -0.75 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 812 TYR 0.014 0.001 TYR A 765 PHE 0.016 0.002 PHE A 653 TRP 0.007 0.001 TRP A 435 HIS 0.007 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 4401) covalent geometry : angle 0.65532 / 0.35 ( 6163) hydrogen bonds : bond 0.05034 / 3.48 ( 154) hydrogen bonds : angle 5.54457 / 3.81 ( 416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.118 Fit side-chains REVERT: A 447 GLU cc_start: 0.6224 (tm-30) cc_final: 0.5900 (tm-30) REVERT: A 549 MET cc_start: 0.5667 (tpp) cc_final: 0.4462 (ptm) REVERT: A 804 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6445 (m-80) outliers start: 19 outliers final: 10 residues processed: 57 average time/residue: 0.4385 time to fit residues: 26.0606 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 807 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.253337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.198335 restraints weight = 4735.782| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.54 r_work: 0.4217 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4401 Z= 0.145 Angle : 0.624 8.148 6163 Z= 0.339 Chirality : 0.047 0.215 727 Planarity : 0.005 0.044 639 Dihedral : 23.395 174.190 1101 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.26 % Allowed : 31.86 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.42), residues: 415 helix: 0.47 (0.44), residues: 141 sheet: -1.58 (0.49), residues: 89 loop : -0.64 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 630 TYR 0.012 0.001 TYR A 765 PHE 0.015 0.001 PHE A 653 TRP 0.006 0.001 TRP A 435 HIS 0.005 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 4401) covalent geometry : angle 0.62351 / 0.34 ( 6163) hydrogen bonds : bond 0.04628 / 3.16 ( 154) hydrogen bonds : angle 5.45456 / 3.76 ( 416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.082 Fit side-chains REVERT: A 447 GLU cc_start: 0.6292 (tm-30) cc_final: 0.5992 (tm-30) REVERT: A 549 MET cc_start: 0.5589 (tpp) cc_final: 0.4361 (ptm) REVERT: A 553 GLN cc_start: 0.5672 (mm-40) cc_final: 0.5162 (mt0) REVERT: A 617 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.7164 (p) REVERT: A 804 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6370 (m-80) outliers start: 19 outliers final: 8 residues processed: 55 average time/residue: 0.3415 time to fit residues: 19.8335 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 ASN A 807 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.245498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.190306 restraints weight = 4766.237| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.43 r_work: 0.4158 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4401 Z= 0.232 Angle : 0.728 8.523 6163 Z= 0.387 Chirality : 0.050 0.218 727 Planarity : 0.006 0.041 639 Dihedral : 23.278 174.633 1099 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.37 % Allowed : 31.30 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.42), residues: 415 helix: 0.21 (0.43), residues: 141 sheet: -1.61 (0.51), residues: 91 loop : -0.69 (0.51), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 663 TYR 0.033 0.003 TYR A 765 PHE 0.021 0.003 PHE A 659 TRP 0.008 0.002 TRP A 435 HIS 0.009 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 ( 4401) covalent geometry : angle 0.72755 / 0.39 ( 6163) hydrogen bonds : bond 0.05726 / 3.89 ( 154) hydrogen bonds : angle 5.69423 / 3.98 ( 416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 37 time to evaluate : 0.139 Fit side-chains REVERT: A 447 GLU cc_start: 0.6359 (tm-30) cc_final: 0.6028 (tm-30) REVERT: A 549 MET cc_start: 0.5651 (tpp) cc_final: 0.4572 (ptm) REVERT: A 705 ILE cc_start: 0.7567 (mt) cc_final: 0.7311 (mp) REVERT: A 804 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6582 (m-80) outliers start: 23 outliers final: 14 residues processed: 55 average time/residue: 0.3749 time to fit residues: 21.6808 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 17 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 459 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.252465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.198526 restraints weight = 4882.370| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.48 r_work: 0.4235 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4401 Z= 0.130 Angle : 0.601 7.232 6163 Z= 0.328 Chirality : 0.046 0.219 727 Planarity : 0.004 0.037 639 Dihedral : 23.127 173.052 1099 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.16 % Allowed : 32.96 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.43), residues: 415 helix: 0.62 (0.43), residues: 141 sheet: -1.57 (0.51), residues: 89 loop : -0.57 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 663 TYR 0.010 0.001 TYR A 804 PHE 0.015 0.002 PHE A 659 TRP 0.007 0.001 TRP A 769 HIS 0.007 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4401) covalent geometry : angle 0.60059 / 0.33 ( 6163) hydrogen bonds : bond 0.04536 / 3.07 ( 154) hydrogen bonds : angle 5.39782 / 3.76 ( 416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.125 Fit side-chains REVERT: A 447 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5745 (tm-30) REVERT: A 549 MET cc_start: 0.5377 (tpp) cc_final: 0.4427 (ptm) REVERT: A 607 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6329 (mtmm) REVERT: A 617 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.6837 (p) REVERT: A 804 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6648 (m-80) outliers start: 15 outliers final: 5 residues processed: 50 average time/residue: 0.4234 time to fit residues: 22.2071 Evaluate side-chains 43 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 10.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.252184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.197959 restraints weight = 4932.540| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.48 r_work: 0.4231 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4401 Z= 0.140 Angle : 0.613 6.989 6163 Z= 0.331 Chirality : 0.046 0.217 727 Planarity : 0.005 0.038 639 Dihedral : 23.005 173.479 1099 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.88 % Allowed : 33.80 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.42), residues: 415 helix: 0.52 (0.43), residues: 141 sheet: -1.52 (0.51), residues: 89 loop : -0.54 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 630 TYR 0.012 0.001 TYR A 765 PHE 0.014 0.002 PHE A 659 TRP 0.007 0.001 TRP A 769 HIS 0.005 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4401) covalent geometry : angle 0.61318 / 0.33 ( 6163) hydrogen bonds : bond 0.04530 / 3.07 ( 154) hydrogen bonds : angle 5.40267 / 3.78 ( 416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.135 Fit side-chains REVERT: A 483 MET cc_start: 0.7146 (ttp) cc_final: 0.6808 (ttp) REVERT: A 549 MET cc_start: 0.5420 (tpp) cc_final: 0.4434 (ptm) REVERT: A 607 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6333 (mtmm) REVERT: A 804 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: A 807 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7423 (t-170) outliers start: 14 outliers final: 7 residues processed: 46 average time/residue: 0.3781 time to fit residues: 18.3652 Evaluate side-chains 41 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 40.0000 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 40.0000 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.254328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.200547 restraints weight = 4807.896| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.47 r_work: 0.4246 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4401 Z= 0.133 Angle : 0.604 6.873 6163 Z= 0.328 Chirality : 0.046 0.216 727 Planarity : 0.004 0.038 639 Dihedral : 22.920 174.055 1099 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.43 % Allowed : 31.86 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.42), residues: 415 helix: 0.52 (0.43), residues: 141 sheet: -1.52 (0.50), residues: 89 loop : -0.56 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 423 TYR 0.012 0.001 TYR A 765 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.010 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4401) covalent geometry : angle 0.60446 / 0.33 ( 6163) hydrogen bonds : bond 0.04548 / 3.03 ( 154) hydrogen bonds : angle 5.40398 / 3.78 ( 416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.135 Fit side-chains REVERT: A 483 MET cc_start: 0.7074 (ttp) cc_final: 0.6740 (ttp) REVERT: A 549 MET cc_start: 0.5368 (tpp) cc_final: 0.4395 (ptm) REVERT: A 607 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6335 (mtmm) REVERT: A 804 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6383 (m-80) outliers start: 16 outliers final: 10 residues processed: 48 average time/residue: 0.4171 time to fit residues: 20.9643 Evaluate side-chains 46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 774 PHE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.251786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195973 restraints weight = 4826.712| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.49 r_work: 0.4207 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4401 Z= 0.142 Angle : 0.609 7.339 6163 Z= 0.329 Chirality : 0.046 0.213 727 Planarity : 0.005 0.037 639 Dihedral : 22.844 173.767 1099 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.43 % Allowed : 31.86 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.42), residues: 415 helix: 0.63 (0.44), residues: 140 sheet: -1.63 (0.50), residues: 89 loop : -0.59 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 647 TYR 0.018 0.002 TYR A 765 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.008 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4401) covalent geometry : angle 0.60864 / 0.33 ( 6163) hydrogen bonds : bond 0.04804 / 3.20 ( 154) hydrogen bonds : angle 5.42873 / 3.80 ( 416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 MET cc_start: 0.5404 (tpp) cc_final: 0.4342 (ptm) REVERT: A 607 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6328 (mtmm) REVERT: A 804 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6186 (m-80) outliers start: 16 outliers final: 12 residues processed: 50 average time/residue: 0.4268 time to fit residues: 22.4373 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN A 699 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.252510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.197349 restraints weight = 4823.270| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.49 r_work: 0.4218 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4401 Z= 0.140 Angle : 0.620 7.056 6163 Z= 0.337 Chirality : 0.046 0.213 727 Planarity : 0.005 0.062 639 Dihedral : 22.821 174.001 1099 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.88 % Allowed : 32.69 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.42), residues: 415 helix: 0.58 (0.43), residues: 140 sheet: -1.51 (0.50), residues: 94 loop : -0.62 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 812 TYR 0.014 0.001 TYR A 765 PHE 0.021 0.002 PHE A 811 TRP 0.008 0.001 TRP A 769 HIS 0.011 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4401) covalent geometry : angle 0.62010 / 0.34 ( 6163) hydrogen bonds : bond 0.04653 / 3.09 ( 154) hydrogen bonds : angle 5.37533 / 3.77 ( 416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 483 MET cc_start: 0.7099 (ttp) cc_final: 0.6793 (ttp) REVERT: A 549 MET cc_start: 0.5361 (tpp) cc_final: 0.4335 (ptm) REVERT: A 607 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6307 (mtmm) REVERT: A 804 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: A 811 PHE cc_start: 0.7367 (m-80) cc_final: 0.6749 (m-80) outliers start: 14 outliers final: 12 residues processed: 45 average time/residue: 0.4205 time to fit residues: 19.8651 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 699 GLN Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 TRP Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 GLN A 699 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.252863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.197580 restraints weight = 4803.160| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 2.55 r_work: 0.4209 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4401 Z= 0.145 Angle : 0.631 9.084 6163 Z= 0.346 Chirality : 0.046 0.212 727 Planarity : 0.005 0.057 639 Dihedral : 22.806 173.922 1099 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.26 % Allowed : 31.30 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.42), residues: 415 helix: 0.49 (0.43), residues: 140 sheet: -1.49 (0.50), residues: 94 loop : -0.63 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 812 TYR 0.015 0.002 TYR A 804 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.024 0.002 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 4401) covalent geometry : angle 0.63102 / 0.35 ( 6163) hydrogen bonds : bond 0.04733 / 3.10 ( 154) hydrogen bonds : angle 5.41956 / 3.80 ( 416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.77 seconds wall clock time: 24 minutes 3.60 seconds (1443.60 seconds total)