Starting phenix.real_space_refine on Tue Aug 4 14:43:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6t_62135/08_2026/9k6t_62135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6t_62135/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k6t_62135/08_2026/9k6t_62135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6t_62135/08_2026/9k6t_62135.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k6t_62135/08_2026/9k6t_62135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6t_62135/08_2026/9k6t_62135.map" } 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-2.2rc3-6140/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: 0.92, per 1000 atoms: 0.22 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: 0.23 Conformation dependent library (CDL) restraints added in 78.0 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: 0.37 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: 0.42 Time building geometry restraints manager: 0.30 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=" P A C 5 " pdb=" O5' A C 5 " ideal model delta sigma weight residual 1.593 1.625 -0.032 1.00e-02 1.00e+04 1.02e+01 ... (remaining 4396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 5933 2.81 - 5.62: 177 5.62 - 8.43: 44 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=" C3' A C 10 " pdb=" C2' A C 10 " pdb=" C1' A C 10 " ideal model delta sigma weight residual 101.30 97.07 4.23 7.00e-01 2.04e+00 3.66e+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 ... (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: 634 0.111 - 0.222: 67 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.600 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- 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 : 0.008 0.165 4401 Z= 0.452 Angle : 1.222 14.042 6163 Z= 0.747 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 0.00751 / 0.45 ( 4401) covalent geometry : angle 1.22208 / 0.75 ( 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 : 0.140 Fit side-chains REVERT: A 761 ARG cc_start: 0.4986 (OUTLIER) cc_final: 0.3624 (mtp180) 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: 0.6584 time to fit residues: 36.6919 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 : 0.082 ------------------------------------------------------------------------------- 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 = 0.4780 r_free = 0.4780 target = 0.253469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.199884 restraints weight = 4788.986| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.52 r_work: 0.4231 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.1409 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= 0.160 Angle : 0.699 9.805 6163 Z= 0.379 Chirality : 0.050 0.293 727 Planarity : 0.006 0.055 639 Dihedral : 23.712 177.760 1109 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.71 % Allowed : 26.04 % Favored : 69.25 % 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: -1.27 (0.40), residues: 415 helix: -0.02 (0.43), residues: 140 sheet: -1.66 (0.49), residues: 85 loop : -0.93 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 710 TYR 0.016 0.002 TYR A 765 PHE 0.014 0.001 PHE A 653 TRP 0.009 0.001 TRP A 435 HIS 0.012 0.002 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 4401) covalent geometry : angle 0.69939 / 0.38 ( 6163) hydrogen bonds : bond 0.05428 / 3.65 ( 154) hydrogen bonds : angle 5.85638 / 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 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.150 Fit side-chains REVERT: A 447 GLU cc_start: 0.6104 (tm-30) cc_final: 0.5795 (tm-30) REVERT: A 549 MET cc_start: 0.5363 (tpp) cc_final: 0.4314 (ptm) REVERT: A 804 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6196 (m-80) outliers start: 17 outliers final: 8 residues processed: 57 average time/residue: 0.4194 time to fit residues: 25.1984 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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: 0.0030 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 = 0.4755 r_free = 0.4755 target = 0.250489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.195974 restraints weight = 4747.518| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.51 r_work: 0.4187 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4401 Z= 0.173 Angle : 0.687 9.913 6163 Z= 0.366 Chirality : 0.049 0.262 727 Planarity : 0.006 0.046 639 Dihedral : 23.420 175.013 1101 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.54 % Allowed : 29.92 % Favored : 64.54 % 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: -1.01 (0.42), residues: 415 helix: 0.17 (0.43), residues: 141 sheet: -1.54 (0.49), residues: 89 loop : -0.72 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 812 TYR 0.014 0.002 TYR A 765 PHE 0.017 0.002 PHE A 653 TRP 0.008 0.001 TRP A 435 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 4401) covalent geometry : angle 0.68749 / 0.37 ( 6163) hydrogen bonds : bond 0.05413 / 3.72 ( 154) hydrogen bonds : angle 5.57389 / 3.85 ( 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 66 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.086 Fit side-chains REVERT: A 447 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5771 (tm-30) REVERT: A 549 MET cc_start: 0.5747 (tpp) cc_final: 0.4498 (ptm) REVERT: A 747 ASP cc_start: 0.3569 (p0) cc_final: 0.3256 (p0) REVERT: A 804 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: A 807 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7429 (t-170) outliers start: 20 outliers final: 9 residues processed: 60 average time/residue: 0.4167 time to fit residues: 26.1615 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 30.0000 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN A 459 GLN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN 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 = 0.4748 r_free = 0.4748 target = 0.250565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195078 restraints weight = 4742.408| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.51 r_work: 0.4202 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.2138 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= 0.152 Angle : 0.654 8.930 6163 Z= 0.351 Chirality : 0.047 0.246 727 Planarity : 0.005 0.045 639 Dihedral : 23.171 173.881 1101 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.54 % Allowed : 32.41 % Favored : 62.05 % 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: -0.84 (0.42), residues: 415 helix: 0.35 (0.43), residues: 141 sheet: -1.49 (0.49), residues: 89 loop : -0.63 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 812 TYR 0.011 0.001 TYR A 805 PHE 0.016 0.002 PHE A 659 TRP 0.006 0.001 TRP A 435 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4401) covalent geometry : angle 0.65419 / 0.35 ( 6163) hydrogen bonds : bond 0.04821 / 3.29 ( 154) hydrogen bonds : angle 5.51406 / 3.83 ( 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: 20 poor density : 40 time to evaluate : 0.135 Fit side-chains REVERT: A 447 GLU cc_start: 0.6280 (tm-30) cc_final: 0.5960 (tm-30) REVERT: A 549 MET cc_start: 0.5643 (tpp) cc_final: 0.4512 (ptm) REVERT: A 581 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: A 617 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7204 (p) REVERT: A 804 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6305 (m-80) outliers start: 20 outliers final: 9 residues processed: 55 average time/residue: 0.3614 time to fit residues: 20.9493 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 581 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN 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 = 0.4735 r_free = 0.4735 target = 0.247978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.194178 restraints weight = 4747.517| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.43 r_work: 0.4179 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4401 Z= 0.203 Angle : 0.699 7.843 6163 Z= 0.369 Chirality : 0.048 0.248 727 Planarity : 0.006 0.049 639 Dihedral : 23.068 172.708 1101 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.09 % Allowed : 32.13 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.43), residues: 415 helix: 0.30 (0.43), residues: 141 sheet: -1.52 (0.51), residues: 89 loop : -0.66 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 812 TYR 0.022 0.002 TYR A 765 PHE 0.018 0.002 PHE A 811 TRP 0.007 0.002 TRP A 435 HIS 0.010 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 4401) covalent geometry : angle 0.69851 / 0.37 ( 6163) hydrogen bonds : bond 0.05437 / 3.68 ( 154) hydrogen bonds : angle 5.57629 / 3.90 ( 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 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.148 Fit side-chains REVERT: A 447 GLU cc_start: 0.6273 (tm-30) cc_final: 0.5922 (tm-30) REVERT: A 549 MET cc_start: 0.5579 (tpp) cc_final: 0.4491 (ptm) REVERT: A 804 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6524 (m-80) outliers start: 22 outliers final: 13 residues processed: 51 average time/residue: 0.4043 time to fit residues: 21.7579 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 : 0.136 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 43 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 424 ASN ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS A 839 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.255089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.201087 restraints weight = 4847.258| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.52 r_work: 0.4266 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2652 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= 0.131 Angle : 0.607 6.868 6163 Z= 0.329 Chirality : 0.045 0.244 727 Planarity : 0.005 0.043 639 Dihedral : 22.901 174.953 1099 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.99 % Allowed : 34.35 % Favored : 60.66 % 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: -0.64 (0.43), residues: 415 helix: 0.61 (0.43), residues: 141 sheet: -1.49 (0.51), residues: 89 loop : -0.53 (0.52), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 773 TYR 0.011 0.001 TYR A 804 PHE 0.017 0.002 PHE A 811 TRP 0.007 0.001 TRP A 769 HIS 0.006 0.002 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 4401) covalent geometry : angle 0.60669 / 0.33 ( 6163) hydrogen bonds : bond 0.04513 / 3.05 ( 154) hydrogen bonds : angle 5.37755 / 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 56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.164 Fit side-chains REVERT: A 483 MET cc_start: 0.7025 (ttp) cc_final: 0.6660 (ttp) REVERT: A 549 MET cc_start: 0.5323 (tpp) cc_final: 0.4370 (ptm) REVERT: A 607 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6320 (mtmm) REVERT: A 617 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6794 (p) REVERT: A 804 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6517 (m-80) outliers start: 18 outliers final: 5 residues processed: 50 average time/residue: 0.4164 time to fit residues: 21.8948 Evaluate side-chains 40 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.251595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.197399 restraints weight = 4916.027| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 2.45 r_work: 0.4234 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2722 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= 0.147 Angle : 0.637 6.816 6163 Z= 0.338 Chirality : 0.047 0.243 727 Planarity : 0.005 0.056 639 Dihedral : 22.830 174.337 1099 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.43 % Allowed : 34.35 % Favored : 61.22 % 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: -0.75 (0.42), residues: 415 helix: 0.42 (0.43), residues: 141 sheet: -1.49 (0.51), residues: 89 loop : -0.53 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 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 0.010 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4401) covalent geometry : angle 0.63683 / 0.34 ( 6163) hydrogen bonds : bond 0.04696 / 3.15 ( 154) hydrogen bonds : angle 5.45747 / 3.85 ( 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.104 Fit side-chains REVERT: A 549 MET cc_start: 0.5426 (tpp) cc_final: 0.4343 (ptm) REVERT: A 553 GLN cc_start: 0.5591 (mm-40) cc_final: 0.5070 (mt0) REVERT: A 607 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6333 (mtmm) REVERT: A 663 ARG cc_start: 0.6101 (mpp80) cc_final: 0.5890 (mpp80) REVERT: A 804 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6525 (m-80) outliers start: 16 outliers final: 9 residues processed: 50 average time/residue: 0.4427 time to fit residues: 23.2018 Evaluate side-chains 48 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 50.0000 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.251638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.197736 restraints weight = 4834.816| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.44 r_work: 0.4231 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4401 Z= 0.140 Angle : 0.623 7.248 6163 Z= 0.335 Chirality : 0.046 0.240 727 Planarity : 0.005 0.044 639 Dihedral : 22.762 174.569 1099 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.71 % Allowed : 33.52 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.42), residues: 415 helix: 0.53 (0.43), residues: 141 sheet: -1.55 (0.51), residues: 89 loop : -0.58 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 423 TYR 0.013 0.001 TYR A 765 PHE 0.015 0.002 PHE A 659 TRP 0.008 0.001 TRP A 769 HIS 0.006 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 4401) covalent geometry : angle 0.62334 / 0.33 ( 6163) hydrogen bonds : bond 0.04779 / 3.17 ( 154) hydrogen bonds : angle 5.45607 / 3.85 ( 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.141 Fit side-chains REVERT: A 549 MET cc_start: 0.5409 (tpp) cc_final: 0.4422 (ptm) REVERT: A 607 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6347 (mtmm) REVERT: A 804 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6344 (m-80) outliers start: 17 outliers final: 10 residues processed: 49 average time/residue: 0.4553 time to fit residues: 23.3858 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 : 0.141 ------------------------------------------------------------------------------- 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 555 THR Chi-restraints excluded: chain A residue 569 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.0970 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.253368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198869 restraints weight = 4839.963| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.47 r_work: 0.4230 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.2979 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= 0.126 Angle : 0.612 6.633 6163 Z= 0.328 Chirality : 0.045 0.238 727 Planarity : 0.005 0.051 639 Dihedral : 22.709 175.439 1099 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.43 % Allowed : 34.90 % Favored : 60.66 % 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: 0.63 (0.44), residues: 140 sheet: -1.51 (0.50), residues: 94 loop : -0.58 (0.51), residues: 181 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 0.019 0.002 PHE A 811 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 0.00270 / 0.13 ( 4401) covalent geometry : angle 0.61247 / 0.33 ( 6163) hydrogen bonds : bond 0.04650 / 3.07 ( 154) hydrogen bonds : angle 5.40686 / 3.81 ( 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 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 429 THR cc_start: 0.7718 (p) cc_final: 0.7450 (p) REVERT: A 469 SER cc_start: 0.6241 (OUTLIER) cc_final: 0.5970 (p) REVERT: A 549 MET cc_start: 0.5272 (tpp) cc_final: 0.4222 (ptm) REVERT: A 553 GLN cc_start: 0.5406 (mm-40) cc_final: 0.4851 (mt0) REVERT: A 607 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6323 (mtmm) REVERT: A 804 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6216 (m-80) outliers start: 16 outliers final: 12 residues processed: 51 average time/residue: 0.4237 time to fit residues: 22.6908 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 469 SER 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 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: 0.9980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 GLN ** A 764 HIS ** 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 = 0.4761 r_free = 0.4761 target = 0.251232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.195708 restraints weight = 4826.651| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.49 r_work: 0.4207 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4401 Z= 0.159 Angle : 0.651 7.098 6163 Z= 0.348 Chirality : 0.046 0.237 727 Planarity : 0.006 0.072 639 Dihedral : 22.693 174.579 1099 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.26 % Allowed : 33.80 % Favored : 60.94 % 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: -0.75 (0.42), residues: 415 helix: 0.56 (0.44), residues: 140 sheet: -1.56 (0.50), residues: 89 loop : -0.62 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.022 0.002 TYR A 765 PHE 0.023 0.002 PHE A 811 TRP 0.008 0.001 TRP A 769 HIS 0.014 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 4401) covalent geometry : angle 0.65138 / 0.35 ( 6163) hydrogen bonds : bond 0.04800 / 3.16 ( 154) hydrogen bonds : angle 5.48582 / 3.86 ( 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 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.169 Fit side-chains REVERT: A 469 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.6024 (p) REVERT: A 549 MET cc_start: 0.5409 (tpp) cc_final: 0.4378 (ptm) REVERT: A 607 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6376 (mmmt) REVERT: A 804 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6310 (m-80) outliers start: 19 outliers final: 13 residues processed: 51 average time/residue: 0.4258 time to fit residues: 22.8716 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 469 SER 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 767 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 GLN ** A 764 HIS ** 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 = 0.4811 r_free = 0.4811 target = 0.255405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.201190 restraints weight = 4833.648| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.49 r_work: 0.4218 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4401 Z= 0.143 Angle : 0.655 9.339 6163 Z= 0.348 Chirality : 0.046 0.236 727 Planarity : 0.006 0.065 639 Dihedral : 22.680 174.808 1099 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.99 % Allowed : 34.35 % Favored : 60.66 % 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: -0.76 (0.43), residues: 415 helix: 0.61 (0.44), residues: 140 sheet: -1.49 (0.50), residues: 94 loop : -0.70 (0.51), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 812 TYR 0.009 0.001 TYR A 804 PHE 0.019 0.002 PHE A 811 TRP 0.008 0.001 TRP A 769 HIS 0.004 0.001 HIS A 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 4401) covalent geometry : angle 0.65482 / 0.35 ( 6163) hydrogen bonds : bond 0.04769 / 3.13 ( 154) hydrogen bonds : angle 5.44266 / 3.84 ( 416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.96 seconds wall clock time: 24 minutes 47.41 seconds (1487.41 seconds total)