Starting phenix.real_space_refine on Thu Jul 2 03:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6q_62132/07_2026/9k6q_62132.cif" } resolution = 2.7 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= 0.054 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 31 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3867 2.51 5 N 1123 2.21 5 O 1219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 6276 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 358 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "C" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 298 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 9} Chain: "A" Number of atoms: 5619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5619 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 660} Chain breaks: 2 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: 1.57, per 1000 atoms: 0.25 Number of scatterers: 6276 At special positions: 0 Unit cell: (74.1, 76.38, 108.3, 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 35 16.00 P 31 15.00 Mg 1 11.99 O 1219 8.00 N 1123 7.00 C 3867 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: 0.62 Conformation dependent library (CDL) restraints added in 413.4 milliseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 36.0% alpha, 20.0% beta 9 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.564A pdb=" N SER A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.610A pdb=" N SER A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.279A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 571 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.896A pdb=" N ARG A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.530A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.635A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 775 through 788 Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 839 through 844 Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.452A pdb=" N ARG A 854 " --> pdb=" O GLN A 850 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.065A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 598 " --> pdb=" O ALA A 669 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.168A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.009A pdb=" N ILE A 54 " --> pdb=" O CYS A 137 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS A 56 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 129 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 132 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 113 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 removed outlier: 3.976A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1698 1.33 - 1.45: 1259 1.45 - 1.57: 3414 1.57 - 1.69: 60 1.69 - 1.81: 54 Bond restraints: 6485 Sorted by residual: bond pdb=" P A C 4 " pdb=" O5' A C 4 " ideal model delta sigma weight residual 1.593 1.634 -0.041 1.50e-02 4.44e+03 7.33e+00 bond pdb=" O5' A C 4 " pdb=" C5' A C 4 " ideal model delta sigma weight residual 1.424 1.460 -0.036 1.50e-02 4.44e+03 5.85e+00 bond pdb=" N LYS A 355 " pdb=" CA LYS A 355 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.19e-02 7.06e+03 5.83e+00 bond pdb=" N GLN A 757 " pdb=" CA GLN A 757 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" O5' G C 5 " pdb=" C5' G C 5 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.79e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 8818 3.12 - 6.24: 91 6.24 - 9.36: 14 9.36 - 12.48: 1 12.48 - 15.60: 2 Bond angle restraints: 8926 Sorted by residual: angle pdb=" O3' A C 4 " pdb=" C3' A C 4 " pdb=" C2' A C 4 " ideal model delta sigma weight residual 109.50 96.31 13.19 1.50e+00 4.44e-01 7.73e+01 angle pdb=" C3' A C 4 " pdb=" C2' A C 4 " pdb=" C1' A C 4 " ideal model delta sigma weight residual 101.50 95.33 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" C LYS A 709 " pdb=" CA LYS A 709 " pdb=" CB LYS A 709 " ideal model delta sigma weight residual 109.55 119.54 -9.99 1.68e+00 3.54e-01 3.54e+01 angle pdb=" N LYS A 709 " pdb=" CA LYS A 709 " pdb=" C LYS A 709 " ideal model delta sigma weight residual 113.72 106.12 7.60 1.30e+00 5.92e-01 3.42e+01 angle pdb=" N1 C B 9 " pdb=" C2 C B 9 " pdb=" O2 C B 9 " ideal model delta sigma weight residual 118.90 122.32 -3.42 6.00e-01 2.78e+00 3.26e+01 ... (remaining 8921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 3741 35.05 - 70.10: 203 70.10 - 105.15: 20 105.15 - 140.20: 1 140.20 - 175.25: 2 Dihedral angle restraints: 3967 sinusoidal: 1917 harmonic: 2050 Sorted by residual: dihedral pdb=" CA HIS A 621 " pdb=" C HIS A 621 " pdb=" N PRO A 622 " pdb=" CA PRO A 622 " ideal model delta harmonic sigma weight residual -180.00 -113.10 -66.90 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual -128.00 47.25 -175.25 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 58.90 173.10 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 961 0.116 - 0.231: 41 0.231 - 0.347: 1 0.347 - 0.462: 5 0.462 - 0.578: 4 Chirality restraints: 1012 Sorted by residual: chirality pdb=" P A C 4 " pdb=" OP1 A C 4 " pdb=" OP2 A C 4 " pdb=" O5' A C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" P U C 13 " pdb=" OP1 U C 13 " pdb=" OP2 U C 13 " pdb=" O5' U C 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" P U C 14 " pdb=" OP1 U C 14 " pdb=" OP2 U C 14 " pdb=" O5' U C 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 1009 not shown) Planarity restraints: 1041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 175 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 176 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 621 " 0.065 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 622 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 13 " -0.034 2.00e-02 2.50e+03 1.88e-02 7.93e+00 pdb=" N1 U B 13 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U B 13 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U B 13 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U B 13 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U B 13 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U B 13 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U B 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U B 13 " 0.003 2.00e-02 2.50e+03 ... (remaining 1038 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 928 2.76 - 3.30: 5633 3.30 - 3.83: 11560 3.83 - 4.37: 13361 4.37 - 4.90: 21958 Nonbonded interactions: 53440 Sorted by model distance: nonbonded pdb=" O HIS A 507 " pdb=" OG1 THR A 511 " model vdw 2.228 3.040 nonbonded pdb=" O GLN A 496 " pdb=" OG SER A 500 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A 209 " pdb=" O LYS A 212 " model vdw 2.319 3.040 nonbonded pdb=" O LEU A 786 " pdb=" OG1 THR A 789 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A 752 " pdb=" O VAL A 797 " model vdw 2.340 3.040 ... (remaining 53435 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: 0.460 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.004 0.072 6485 Z= 0.229 Angle : 0.826 15.601 8926 Z= 0.505 Chirality : 0.068 0.578 1012 Planarity : 0.008 0.108 1041 Dihedral : 20.247 175.246 2643 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 0.81 % Allowed : 21.17 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.54 (0.31), residues: 700 helix: 0.52 (0.34), residues: 223 sheet: -0.23 (0.39), residues: 174 loop : -1.01 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 658 TYR 0.024 0.002 TYR A 55 PHE 0.013 0.002 PHE A 491 TRP 0.009 0.002 TRP A 199 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.23 ( 6485) covalent geometry : angle 0.82557 / 0.50 ( 8926) hydrogen bonds : bond 0.16733 / 16.00 ( 284) hydrogen bonds : angle 7.63781 / 9.62 ( 781) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.201 Fit side-chains REVERT: A 637 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6467 (tp30) outliers start: 5 outliers final: 1 residues processed: 81 average time/residue: 0.7321 time to fit residues: 61.4830 Evaluate side-chains 65 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.187633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138237 restraints weight = 5929.049| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.56 r_work: 0.3309 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6485 Z= 0.145 Angle : 0.618 7.411 8926 Z= 0.345 Chirality : 0.048 0.388 1012 Planarity : 0.007 0.100 1041 Dihedral : 18.363 176.648 1253 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 22.96 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.18 (0.31), residues: 700 helix: 1.07 (0.35), residues: 228 sheet: -0.32 (0.38), residues: 180 loop : -0.86 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.016 0.001 TYR A 55 PHE 0.015 0.002 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 6485) covalent geometry : angle 0.61845 / 0.34 ( 8926) hydrogen bonds : bond 0.05424 / 5.40 ( 284) hydrogen bonds : angle 5.67022 / 6.94 ( 781) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.192 Fit side-chains REVERT: A 98 LYS cc_start: 0.6310 (mtmm) cc_final: 0.6046 (mptt) REVERT: A 637 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7020 (tp30) outliers start: 12 outliers final: 3 residues processed: 75 average time/residue: 0.6536 time to fit residues: 51.1133 Evaluate side-chains 72 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS A 507 HIS A 623 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.186947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.139607 restraints weight = 5872.070| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.33 r_work: 0.3323 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6485 Z= 0.149 Angle : 0.601 7.272 8926 Z= 0.330 Chirality : 0.047 0.261 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.363 178.282 1251 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.57 % Rotamer: Outliers : 3.42 % Allowed : 21.66 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.13 (0.32), residues: 700 helix: 1.34 (0.35), residues: 222 sheet: -0.42 (0.38), residues: 184 loop : -0.90 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.017 0.001 TYR A 55 PHE 0.015 0.002 PHE A 491 TRP 0.008 0.001 TRP A 435 HIS 0.006 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6485) covalent geometry : angle 0.60112 / 0.33 ( 8926) hydrogen bonds : bond 0.05137 / 5.10 ( 284) hydrogen bonds : angle 5.40949 / 6.69 ( 781) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.220 Fit side-chains REVERT: A 98 LYS cc_start: 0.6239 (mtmm) cc_final: 0.6016 (mptt) REVERT: A 172 MET cc_start: 0.4508 (OUTLIER) cc_final: 0.4195 (ttm) REVERT: A 473 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: A 637 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6953 (tp30) outliers start: 21 outliers final: 9 residues processed: 85 average time/residue: 0.7013 time to fit residues: 62.1473 Evaluate side-chains 80 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.183188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131841 restraints weight = 5917.022| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.35 r_work: 0.3250 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6485 Z= 0.188 Angle : 0.638 8.242 8926 Z= 0.345 Chirality : 0.048 0.263 1012 Planarity : 0.007 0.101 1041 Dihedral : 18.415 177.902 1251 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.14 % Favored : 95.71 % Rotamer: Outliers : 3.91 % Allowed : 19.87 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.18 (0.31), residues: 700 helix: 1.23 (0.35), residues: 228 sheet: -0.45 (0.38), residues: 182 loop : -0.91 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 375 TYR 0.019 0.002 TYR A 55 PHE 0.016 0.002 PHE A 491 TRP 0.010 0.002 TRP A 199 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 ( 6485) covalent geometry : angle 0.63788 / 0.35 ( 8926) hydrogen bonds : bond 0.05259 / 5.11 ( 284) hydrogen bonds : angle 5.41944 / 6.65 ( 781) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.240 Fit side-chains REVERT: A 73 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: A 98 LYS cc_start: 0.6319 (mtmm) cc_final: 0.6064 (mtpp) REVERT: A 133 LYS cc_start: 0.6168 (tppt) cc_final: 0.5783 (tppt) REVERT: A 172 MET cc_start: 0.4704 (OUTLIER) cc_final: 0.4395 (ttm) REVERT: A 473 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: A 637 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7045 (tp30) REVERT: A 693 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7159 (mtpt) outliers start: 24 outliers final: 11 residues processed: 83 average time/residue: 0.6598 time to fit residues: 56.9626 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.183092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135265 restraints weight = 5957.815| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.29 r_work: 0.3258 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6485 Z= 0.199 Angle : 0.650 9.199 8926 Z= 0.351 Chirality : 0.049 0.260 1012 Planarity : 0.007 0.101 1041 Dihedral : 18.444 177.770 1251 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.56 % Allowed : 19.71 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.31), residues: 700 helix: 1.19 (0.35), residues: 228 sheet: -0.35 (0.39), residues: 176 loop : -1.00 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 375 TYR 0.022 0.002 TYR A 55 PHE 0.016 0.002 PHE A 491 TRP 0.010 0.002 TRP A 199 HIS 0.005 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 ( 6485) covalent geometry : angle 0.64967 / 0.35 ( 8926) hydrogen bonds : bond 0.05283 / 5.12 ( 284) hydrogen bonds : angle 5.40687 / 6.64 ( 781) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.239 Fit side-chains REVERT: A 73 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5760 (tm-30) REVERT: A 133 LYS cc_start: 0.6214 (tppt) cc_final: 0.5816 (tppt) REVERT: A 473 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: A 517 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9019 (tp) REVERT: A 637 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7065 (tp30) REVERT: A 641 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7544 (t70) REVERT: A 693 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7015 (mtpt) outliers start: 28 outliers final: 14 residues processed: 87 average time/residue: 0.6430 time to fit residues: 58.3446 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** 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 = 0.4019 r_free = 0.4019 target = 0.185863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134789 restraints weight = 5916.807| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.34 r_work: 0.3286 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6485 Z= 0.124 Angle : 0.585 8.722 8926 Z= 0.315 Chirality : 0.045 0.218 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.340 179.259 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.44 % Allowed : 21.66 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.07 (0.32), residues: 700 helix: 1.50 (0.36), residues: 222 sheet: -0.34 (0.39), residues: 181 loop : -1.01 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 97 TYR 0.020 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6485) covalent geometry : angle 0.58508 / 0.31 ( 8926) hydrogen bonds : bond 0.04637 / 4.58 ( 284) hydrogen bonds : angle 5.19498 / 6.40 ( 781) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: A 133 LYS cc_start: 0.6216 (tppt) cc_final: 0.5810 (tppt) REVERT: A 473 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: A 517 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8987 (tp) REVERT: A 637 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6961 (tp30) REVERT: A 641 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7541 (t0) outliers start: 15 outliers final: 7 residues processed: 79 average time/residue: 0.6360 time to fit residues: 52.3233 Evaluate side-chains 77 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.136822 restraints weight = 5878.680| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.35 r_work: 0.3292 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6485 Z= 0.173 Angle : 0.619 7.693 8926 Z= 0.334 Chirality : 0.047 0.248 1012 Planarity : 0.006 0.098 1041 Dihedral : 18.303 178.297 1251 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.75 % Allowed : 20.52 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.16 (0.32), residues: 700 helix: 1.41 (0.35), residues: 222 sheet: -0.37 (0.39), residues: 177 loop : -1.04 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.020 0.002 TYR A 55 PHE 0.016 0.002 PHE A 491 TRP 0.009 0.002 TRP A 199 HIS 0.004 0.001 HIS A 849 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 6485) covalent geometry : angle 0.61912 / 0.33 ( 8926) hydrogen bonds : bond 0.04937 / 4.75 ( 284) hydrogen bonds : angle 5.25491 / 6.46 ( 781) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.215 Fit side-chains REVERT: A 73 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5756 (tm-30) REVERT: A 133 LYS cc_start: 0.6315 (tppt) cc_final: 0.5931 (tppt) REVERT: A 396 GLU cc_start: 0.7386 (tt0) cc_final: 0.7029 (tt0) REVERT: A 473 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: A 517 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 637 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7028 (tp30) REVERT: A 641 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7509 (t0) outliers start: 23 outliers final: 13 residues processed: 89 average time/residue: 0.6801 time to fit residues: 63.0697 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 818 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.0270 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.185779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138370 restraints weight = 5907.268| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.38 r_work: 0.3312 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6485 Z= 0.137 Angle : 0.588 7.274 8926 Z= 0.317 Chirality : 0.045 0.227 1012 Planarity : 0.006 0.097 1041 Dihedral : 18.279 178.871 1251 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.09 % Allowed : 21.34 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.06 (0.32), residues: 700 helix: 1.51 (0.35), residues: 222 sheet: -0.28 (0.39), residues: 175 loop : -1.02 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.020 0.001 TYR A 55 PHE 0.014 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 6485) covalent geometry : angle 0.58833 / 0.32 ( 8926) hydrogen bonds : bond 0.04650 / 4.51 ( 284) hydrogen bonds : angle 5.14368 / 6.34 ( 781) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.169 Fit side-chains REVERT: A 73 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5740 (tm-30) REVERT: A 98 LYS cc_start: 0.6574 (mtmm) cc_final: 0.6210 (mptt) REVERT: A 133 LYS cc_start: 0.6259 (tppt) cc_final: 0.5864 (tppt) REVERT: A 396 GLU cc_start: 0.7335 (tt0) cc_final: 0.6982 (tt0) REVERT: A 472 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: A 473 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: A 517 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9004 (tp) REVERT: A 637 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7049 (tp30) REVERT: A 641 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7538 (t0) outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 0.6843 time to fit residues: 59.8552 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 678 GLN Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.187490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136133 restraints weight = 5906.901| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.36 r_work: 0.3294 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6485 Z= 0.121 Angle : 0.578 7.437 8926 Z= 0.311 Chirality : 0.044 0.211 1012 Planarity : 0.006 0.096 1041 Dihedral : 18.269 179.713 1251 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.09 % Allowed : 21.17 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -0.02 (0.32), residues: 700 helix: 1.52 (0.36), residues: 223 sheet: -0.34 (0.39), residues: 181 loop : -0.94 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.019 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6485) covalent geometry : angle 0.57842 / 0.31 ( 8926) hydrogen bonds : bond 0.04353 / 4.20 ( 284) hydrogen bonds : angle 5.03373 / 6.20 ( 781) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.227 Fit side-chains REVERT: A 73 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5740 (tm-30) REVERT: A 98 LYS cc_start: 0.6547 (mtmm) cc_final: 0.6143 (mptt) REVERT: A 133 LYS cc_start: 0.6269 (tppt) cc_final: 0.5875 (tppt) REVERT: A 396 GLU cc_start: 0.7301 (tt0) cc_final: 0.6957 (tt0) REVERT: A 472 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7463 (pt0) REVERT: A 473 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: A 517 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9018 (tp) REVERT: A 637 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6949 (tp30) REVERT: A 641 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7480 (t0) outliers start: 19 outliers final: 9 residues processed: 87 average time/residue: 0.6513 time to fit residues: 58.8597 Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 61 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138964 restraints weight = 5880.800| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.36 r_work: 0.3331 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6485 Z= 0.112 Angle : 0.571 7.322 8926 Z= 0.306 Chirality : 0.044 0.192 1012 Planarity : 0.006 0.095 1041 Dihedral : 18.269 179.742 1251 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.61 % Allowed : 22.31 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: 0.06 (0.32), residues: 700 helix: 1.58 (0.35), residues: 224 sheet: -0.30 (0.39), residues: 180 loop : -0.89 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.018 0.001 TYR A 55 PHE 0.012 0.001 PHE A 491 TRP 0.009 0.001 TRP A 435 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6485) covalent geometry : angle 0.57095 / 0.31 ( 8926) hydrogen bonds : bond 0.04136 / 3.98 ( 284) hydrogen bonds : angle 4.90477 / 6.02 ( 781) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.292 Fit side-chains REVERT: A 73 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5727 (tm-30) REVERT: A 98 LYS cc_start: 0.6569 (mtmm) cc_final: 0.6183 (mptt) REVERT: A 133 LYS cc_start: 0.6251 (tppt) cc_final: 0.5852 (tppt) REVERT: A 396 GLU cc_start: 0.7278 (tt0) cc_final: 0.6952 (tt0) REVERT: A 472 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 473 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: A 517 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9001 (tp) REVERT: A 637 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6928 (tp30) outliers start: 16 outliers final: 9 residues processed: 84 average time/residue: 0.6121 time to fit residues: 53.6254 Evaluate side-chains 82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 756 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.188204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136908 restraints weight = 5913.273| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.35 r_work: 0.3302 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6485 Z= 0.132 Angle : 0.598 9.503 8926 Z= 0.315 Chirality : 0.045 0.250 1012 Planarity : 0.006 0.096 1041 Dihedral : 18.323 179.711 1251 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.77 % Allowed : 22.15 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: 0.03 (0.32), residues: 700 helix: 1.51 (0.36), residues: 223 sheet: -0.33 (0.39), residues: 181 loop : -0.84 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 773 TYR 0.018 0.001 TYR A 55 PHE 0.013 0.001 PHE A 491 TRP 0.007 0.001 TRP A 435 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6485) covalent geometry : angle 0.59794 / 0.32 ( 8926) hydrogen bonds : bond 0.04323 / 4.13 ( 284) hydrogen bonds : angle 4.99680 / 6.23 ( 781) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2427.89 seconds wall clock time: 42 minutes 2.64 seconds (2522.64 seconds total)