Starting phenix.real_space_refine on Wed Jul 1 21:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kny_62466/07_2026/9kny_62466.map" } resolution = 3.4 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 89 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PC8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.41 Number of scatterers: 2747 At special positions: 0 Unit cell: (81.51, 93.48, 86.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.35 Conformation dependent library (CDL) restraints added in 122.8 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 60.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 57 removed outlier: 3.789A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.688A pdb=" N HIS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.988A pdb=" N MET A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.055A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 46 No H-bonds generated for 'chain 'A' and resid 45 through 46' Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.647A pdb=" N ILE A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 removed outlier: 3.695A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.514A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.104A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.23 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 780 1.43 - 1.56: 1578 1.56 - 1.68: 18 1.68 - 1.81: 29 Bond restraints: 2814 Sorted by residual: bond pdb=" CA5 CDL B 201 " pdb=" OA6 CDL B 201 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" CB5 CDL B 201 " pdb=" OB6 CDL B 201 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CA7 CDL B 201 " pdb=" OA8 CDL B 201 " ideal model delta sigma weight residual 1.331 1.430 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CB7 CDL B 201 " pdb=" OB8 CDL B 201 " ideal model delta sigma weight residual 1.339 1.436 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C60 CDL B 201 " pdb=" C61 CDL B 201 " ideal model delta sigma weight residual 1.527 1.605 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 3729 3.13 - 6.25: 45 6.25 - 9.38: 4 9.38 - 12.51: 6 12.51 - 15.63: 3 Bond angle restraints: 3787 Sorted by residual: angle pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sigma weight residual 93.28 108.91 -15.63 3.00e+00 1.11e-01 2.72e+01 angle pdb=" OB2 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB5 CDL B 201 " ideal model delta sigma weight residual 96.70 109.87 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" OA3 CDL B 201 " pdb=" PA1 CDL B 201 " pdb=" OA4 CDL B 201 " ideal model delta sigma weight residual 121.92 109.38 12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" OB3 CDL B 201 " pdb=" PB2 CDL B 201 " pdb=" OB4 CDL B 201 " ideal model delta sigma weight residual 121.80 109.47 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O1 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O2 PC8 A 201 " ideal model delta sigma weight residual 119.59 109.01 10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.66: 1566 29.66 - 59.32: 137 59.32 - 88.98: 5 88.98 - 118.64: 0 118.64 - 148.30: 1 Dihedral angle restraints: 1709 sinusoidal: 750 harmonic: 959 Sorted by residual: dihedral pdb=" C1 PC8 A 201 " pdb=" O3 PC8 A 201 " pdb=" P1 PC8 A 201 " pdb=" O4 PC8 A 201 " ideal model delta sinusoidal sigma weight residual 166.83 -44.87 -148.30 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual -86.00 -118.46 32.46 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA GLU A 49 " pdb=" CB GLU A 49 " pdb=" CG GLU A 49 " pdb=" CD GLU A 49 " ideal model delta sinusoidal sigma weight residual 60.00 118.30 -58.30 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 282 0.042 - 0.083: 84 0.083 - 0.124: 19 0.124 - 0.165: 5 0.165 - 0.207: 2 Chirality restraints: 392 Sorted by residual: chirality pdb=" C7 PC8 A 201 " pdb=" C6 PC8 A 201 " pdb=" C8 PC8 A 201 " pdb=" O7 PC8 A 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 67 " pdb=" N MET A 67 " pdb=" C MET A 67 " pdb=" CB MET A 67 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA VAL C 93 " pdb=" N VAL C 93 " pdb=" C VAL C 93 " pdb=" CB VAL C 93 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 34 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 35 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 35 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 35 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 29 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 30 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 25 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.021 5.00e-02 4.00e+02 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 856 2.82 - 3.34: 2545 3.34 - 3.86: 4582 3.86 - 4.38: 5208 4.38 - 4.90: 8671 Nonbonded interactions: 21862 Sorted by model distance: nonbonded pdb=" NH1 ARG C 38 " pdb=" OD1 ASP C 90 " model vdw 2.299 3.120 nonbonded pdb=" NE2 GLN C 13 " pdb=" O SER C 114 " model vdw 2.326 3.120 nonbonded pdb=" NE1 TRP B 82 " pdb=" O GLY A 29 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP C 52 " pdb=" N SER C 57 " model vdw 2.339 3.120 nonbonded pdb=" N ASP A 17 " pdb=" OD1 ASP A 17 " model vdw 2.354 3.120 ... (remaining 21857 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: 3.820 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: 0.120 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 4.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.107 2815 Z= 0.400 Angle : 1.021 15.635 3789 Z= 0.482 Chirality : 0.044 0.207 392 Planarity : 0.005 0.045 464 Dihedral : 19.406 148.303 1092 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.44 % Allowed : 16.67 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.33 (0.42), residues: 327 helix: -0.36 (0.35), residues: 169 sheet: -1.23 (0.64), residues: 57 loop : -1.25 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 97 TYR 0.018 0.002 TYR C 95 PHE 0.026 0.002 PHE A 69 TRP 0.013 0.002 TRP A 28 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.40 ( 2814) covalent geometry : angle 1.02143 / 0.48 ( 3787) SS BOND : bond 0.00508 / 0.27 ( 1) SS BOND : angle 1.10010 / 0.64 ( 2) hydrogen bonds : bond 0.11793 / 7.68 ( 166) hydrogen bonds : angle 5.50693 / 4.08 ( 465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7775 (tt0) REVERT: A 18 PHE cc_start: 0.6371 (t80) cc_final: 0.6046 (p90) REVERT: A 91 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7359 (mm-40) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.0533 time to fit residues: 5.6276 Evaluate side-chains 85 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156006 restraints weight = 4089.553| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.16 r_work: 0.3743 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2815 Z= 0.118 Angle : 0.542 7.149 3789 Z= 0.278 Chirality : 0.040 0.130 392 Planarity : 0.005 0.055 464 Dihedral : 16.425 112.370 510 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.44 % Allowed : 23.33 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.61 (0.46), residues: 327 helix: 1.48 (0.38), residues: 178 sheet: -1.14 (0.71), residues: 50 loop : -0.63 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 113 TYR 0.011 0.001 TYR B 32 PHE 0.011 0.001 PHE A 69 TRP 0.021 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 2814) covalent geometry : angle 0.54113 / 0.28 ( 3787) SS BOND : bond 0.00646 / 0.34 ( 1) SS BOND : angle 1.08797 / 0.58 ( 2) hydrogen bonds : bond 0.03525 / 2.60 ( 166) hydrogen bonds : angle 4.39296 / 3.12 ( 465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 LYS cc_start: 0.7672 (tttt) cc_final: 0.7472 (tppt) REVERT: B 119 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7601 (tt0) REVERT: C 29 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.6839 (p) REVERT: C 43 LYS cc_start: 0.6506 (ttpt) cc_final: 0.6288 (ttpt) REVERT: C 76 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6108 (pttp) REVERT: C 81 LEU cc_start: 0.7864 (tt) cc_final: 0.7604 (tp) REVERT: C 102 TRP cc_start: 0.6127 (t-100) cc_final: 0.5731 (m-90) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.0649 time to fit residues: 5.9130 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 54 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.159133 restraints weight = 3903.155| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.89 r_work: 0.3759 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2815 Z= 0.120 Angle : 0.524 7.004 3789 Z= 0.267 Chirality : 0.040 0.128 392 Planarity : 0.006 0.069 464 Dihedral : 14.513 81.142 496 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.30 % Allowed : 23.33 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.48), residues: 327 helix: 1.92 (0.39), residues: 180 sheet: -1.44 (0.70), residues: 50 loop : -0.03 (0.67), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 72 TYR 0.010 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.017 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 2814) covalent geometry : angle 0.52441 / 0.27 ( 3787) SS BOND : bond 0.01575 / 0.83 ( 1) SS BOND : angle 0.61451 / 0.36 ( 2) hydrogen bonds : bond 0.03375 / 2.46 ( 166) hydrogen bonds : angle 4.30927 / 3.06 ( 465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7602 (tt0) REVERT: A 19 ARG cc_start: 0.7800 (ptt-90) cc_final: 0.6891 (ptt-90) REVERT: A 66 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8676 (t80) REVERT: C 4 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7386 (tp) REVERT: C 81 LEU cc_start: 0.7741 (tt) cc_final: 0.7120 (tp) REVERT: C 102 TRP cc_start: 0.6213 (t-100) cc_final: 0.5885 (m-90) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.0648 time to fit residues: 5.7305 Evaluate side-chains 79 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.193347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158271 restraints weight = 3893.297| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.87 r_work: 0.3763 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2815 Z= 0.125 Angle : 0.517 8.098 3789 Z= 0.264 Chirality : 0.040 0.127 392 Planarity : 0.005 0.060 464 Dihedral : 13.405 68.116 495 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.04 % Allowed : 24.07 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.42 (0.49), residues: 327 helix: 2.06 (0.39), residues: 180 sheet: -1.31 (0.73), residues: 50 loop : 0.22 (0.69), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 19 TYR 0.013 0.001 TYR C 95 PHE 0.015 0.001 PHE A 69 TRP 0.016 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 2814) covalent geometry : angle 0.51695 / 0.26 ( 3787) SS BOND : bond 0.00634 / 0.33 ( 1) SS BOND : angle 0.55435 / 0.33 ( 2) hydrogen bonds : bond 0.03350 / 2.43 ( 166) hydrogen bonds : angle 4.20542 / 2.97 ( 465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7612 (tt0) REVERT: A 19 ARG cc_start: 0.7820 (ptt-90) cc_final: 0.6956 (ptt-90) REVERT: C 4 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7466 (tp) REVERT: C 43 LYS cc_start: 0.6416 (ttpt) cc_final: 0.6207 (ttpt) REVERT: C 81 LEU cc_start: 0.7372 (tt) cc_final: 0.7067 (tp) outliers start: 19 outliers final: 14 residues processed: 75 average time/residue: 0.0726 time to fit residues: 6.2854 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN ** C 82 GLN ** 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 = 0.4232 r_free = 0.4232 target = 0.193372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158604 restraints weight = 3861.384| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.83 r_work: 0.3766 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2815 Z= 0.121 Angle : 0.510 8.772 3789 Z= 0.260 Chirality : 0.040 0.125 392 Planarity : 0.005 0.059 464 Dihedral : 12.899 64.996 495 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 8.89 % Allowed : 21.85 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.58 (0.49), residues: 327 helix: 2.13 (0.39), residues: 180 sheet: -1.17 (0.80), residues: 43 loop : 0.22 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.012 0.001 TYR C 95 PHE 0.015 0.001 PHE A 69 TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2814) covalent geometry : angle 0.50971 / 0.26 ( 3787) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.67171 / 0.39 ( 2) hydrogen bonds : bond 0.03376 / 2.45 ( 166) hydrogen bonds : angle 4.13022 / 2.90 ( 465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7625 (tt0) REVERT: A 102 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: C 43 LYS cc_start: 0.6409 (ttpt) cc_final: 0.6200 (ttpt) REVERT: C 51 ILE cc_start: 0.8426 (tt) cc_final: 0.8112 (mt) REVERT: C 81 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6889 (tp) outliers start: 24 outliers final: 19 residues processed: 75 average time/residue: 0.0776 time to fit residues: 6.7414 Evaluate side-chains 81 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.193517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158284 restraints weight = 3862.435| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.86 r_work: 0.3740 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2815 Z= 0.131 Angle : 0.532 9.182 3789 Z= 0.267 Chirality : 0.040 0.127 392 Planarity : 0.005 0.057 464 Dihedral : 12.671 63.301 495 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 8.15 % Allowed : 22.59 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.59 (0.49), residues: 327 helix: 2.18 (0.39), residues: 180 sheet: -1.31 (0.78), residues: 43 loop : 0.23 (0.67), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 19 TYR 0.013 0.001 TYR C 95 PHE 0.015 0.001 PHE A 69 TRP 0.011 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 2814) covalent geometry : angle 0.53199 / 0.27 ( 3787) SS BOND : bond 0.00703 / 0.37 ( 1) SS BOND : angle 0.84794 / 0.50 ( 2) hydrogen bonds : bond 0.03295 / 2.41 ( 166) hydrogen bonds : angle 4.18194 / 2.93 ( 465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7642 (tt0) REVERT: A 19 ARG cc_start: 0.7833 (ptt-90) cc_final: 0.6973 (ptt-90) REVERT: A 102 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: C 81 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6878 (tp) outliers start: 22 outliers final: 18 residues processed: 75 average time/residue: 0.0665 time to fit residues: 5.8148 Evaluate side-chains 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** 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 = 0.4255 r_free = 0.4255 target = 0.195851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.161394 restraints weight = 3811.304| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.81 r_work: 0.3784 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2815 Z= 0.109 Angle : 0.532 8.414 3789 Z= 0.266 Chirality : 0.041 0.183 392 Planarity : 0.005 0.058 464 Dihedral : 12.321 62.228 495 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 7.04 % Allowed : 23.33 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.77 (0.49), residues: 327 helix: 2.47 (0.39), residues: 176 sheet: -1.32 (0.76), residues: 43 loop : 0.14 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 19 TYR 0.011 0.001 TYR C 95 PHE 0.012 0.001 PHE A 69 TRP 0.010 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 2814) covalent geometry : angle 0.53222 / 0.27 ( 3787) SS BOND : bond 0.00507 / 0.27 ( 1) SS BOND : angle 0.80286 / 0.47 ( 2) hydrogen bonds : bond 0.03188 / 2.31 ( 166) hydrogen bonds : angle 4.10476 / 2.85 ( 465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7283 (ttp80) cc_final: 0.7024 (ptt90) REVERT: B 119 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7647 (tt0) REVERT: A 19 ARG cc_start: 0.7820 (ptt-90) cc_final: 0.6999 (ptt-90) REVERT: A 66 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8717 (t80) REVERT: A 102 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: C 43 LYS cc_start: 0.6383 (ttpt) cc_final: 0.6156 (tttm) REVERT: C 51 ILE cc_start: 0.8408 (tt) cc_final: 0.8022 (mt) REVERT: C 81 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6782 (tp) outliers start: 19 outliers final: 14 residues processed: 70 average time/residue: 0.0658 time to fit residues: 5.3830 Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.194454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.159192 restraints weight = 3893.020| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.89 r_work: 0.3795 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2815 Z= 0.113 Angle : 0.527 8.569 3789 Z= 0.264 Chirality : 0.041 0.200 392 Planarity : 0.005 0.057 464 Dihedral : 12.051 60.873 495 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 6.30 % Allowed : 25.19 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.72 (0.48), residues: 327 helix: 2.44 (0.38), residues: 176 sheet: -1.46 (0.71), residues: 43 loop : 0.17 (0.66), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.012 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.009 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 2814) covalent geometry : angle 0.52700 / 0.26 ( 3787) SS BOND : bond 0.00554 / 0.29 ( 1) SS BOND : angle 0.51180 / 0.30 ( 2) hydrogen bonds : bond 0.03236 / 2.33 ( 166) hydrogen bonds : angle 4.02566 / 2.80 ( 465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7289 (ttp80) cc_final: 0.7028 (ptt90) REVERT: B 119 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7628 (tt0) REVERT: A 19 ARG cc_start: 0.7835 (ptt-90) cc_final: 0.7004 (ptt-90) REVERT: A 102 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5561 (mp0) REVERT: C 43 LYS cc_start: 0.6380 (ttpt) cc_final: 0.6139 (tttm) REVERT: C 51 ILE cc_start: 0.8405 (tt) cc_final: 0.8083 (mt) REVERT: C 81 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6674 (tp) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 0.0863 time to fit residues: 6.9159 Evaluate side-chains 75 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 40.0000 chunk 25 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** 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 = 0.4264 r_free = 0.4264 target = 0.196242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.161478 restraints weight = 3945.345| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.87 r_work: 0.3806 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2815 Z= 0.110 Angle : 0.549 10.475 3789 Z= 0.273 Chirality : 0.041 0.205 392 Planarity : 0.005 0.056 464 Dihedral : 11.715 60.686 492 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 5.19 % Allowed : 24.44 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.68 (0.49), residues: 327 helix: 2.43 (0.38), residues: 176 sheet: -1.53 (0.74), residues: 41 loop : 0.10 (0.66), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 19 TYR 0.013 0.001 TYR C 80 PHE 0.010 0.001 PHE A 69 TRP 0.008 0.001 TRP C 36 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 2814) covalent geometry : angle 0.54929 / 0.27 ( 3787) SS BOND : bond 0.00517 / 0.27 ( 1) SS BOND : angle 0.82515 / 0.48 ( 2) hydrogen bonds : bond 0.03247 / 2.35 ( 166) hydrogen bonds : angle 4.00391 / 2.76 ( 465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6996 (ptt90) REVERT: B 119 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7639 (tt0) REVERT: A 19 ARG cc_start: 0.7835 (ptt-90) cc_final: 0.7019 (ptt-90) REVERT: C 43 LYS cc_start: 0.6432 (ttpt) cc_final: 0.6190 (tttm) REVERT: C 51 ILE cc_start: 0.8430 (tt) cc_final: 0.8085 (mt) REVERT: C 81 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6691 (tp) outliers start: 14 outliers final: 12 residues processed: 63 average time/residue: 0.0702 time to fit residues: 5.1637 Evaluate side-chains 71 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 0.0870 chunk 29 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.202530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168300 restraints weight = 3866.020| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.86 r_work: 0.3858 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2815 Z= 0.101 Angle : 0.530 9.914 3789 Z= 0.267 Chirality : 0.040 0.158 392 Planarity : 0.004 0.057 464 Dihedral : 11.163 60.788 492 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.70 % Allowed : 26.30 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.78 (0.48), residues: 327 helix: 2.43 (0.38), residues: 176 sheet: -1.49 (0.74), residues: 41 loop : 0.30 (0.67), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.009 0.001 TYR C 95 PHE 0.007 0.001 PHE A 69 TRP 0.009 0.001 TRP C 36 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 2814) covalent geometry : angle 0.53011 / 0.27 ( 3787) SS BOND : bond 0.00296 / 0.16 ( 1) SS BOND : angle 0.61908 / 0.35 ( 2) hydrogen bonds : bond 0.03208 / 2.33 ( 166) hydrogen bonds : angle 3.92514 / 2.69 ( 465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7639 (tt0) REVERT: A 19 ARG cc_start: 0.7840 (ptt-90) cc_final: 0.7116 (ptt-90) REVERT: C 51 ILE cc_start: 0.8427 (tt) cc_final: 0.8178 (mt) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.0523 time to fit residues: 3.9001 Evaluate side-chains 64 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.198251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161419 restraints weight = 3979.669| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.15 r_work: 0.3802 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2815 Z= 0.126 Angle : 0.592 10.743 3789 Z= 0.296 Chirality : 0.042 0.169 392 Planarity : 0.005 0.056 464 Dihedral : 11.316 60.986 492 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.33 % Allowed : 25.93 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.66 (0.48), residues: 327 helix: 2.28 (0.38), residues: 176 sheet: -1.47 (0.73), residues: 41 loop : 0.31 (0.67), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 19 TYR 0.012 0.001 TYR C 80 PHE 0.013 0.001 PHE A 69 TRP 0.013 0.001 TRP C 36 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 2814) covalent geometry : angle 0.59238 / 0.30 ( 3787) SS BOND : bond 0.00498 / 0.26 ( 1) SS BOND : angle 0.33106 / 0.19 ( 2) hydrogen bonds : bond 0.03386 / 2.44 ( 166) hydrogen bonds : angle 4.02100 / 2.80 ( 465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 915.20 seconds wall clock time: 16 minutes 22.34 seconds (982.34 seconds total)