Starting phenix.real_space_refine on Sat May 2 10:29:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.map" model { file = "/net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vib_65082/05_2026/9vib_65082.cif" } resolution = 2.26 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= 0.103 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 Fe 4 7.16 5 S 12 5.16 5 C 2906 2.51 5 N 766 2.21 5 O 798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4486 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1084 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 0.75, per 1000 atoms: 0.17 Number of scatterers: 4486 At special positions: 0 Unit cell: (70.38, 84.66, 65.28, 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) Fe 4 26.01 S 12 16.00 O 798 8.00 N 766 7.00 C 2906 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 113.8 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.511A pdb=" N GLY A 18 " --> pdb=" O TRP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.514A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 4.016A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.982A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.527A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.755A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 3 through 18 removed outlier: 3.511A pdb=" N GLY C 18 " --> pdb=" O TRP C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.514A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.016A pdb=" N LYS D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 3.982A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.527A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.755A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 142 336 hydrogen bonds defined for protein. 954 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: 0.38 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 1838 1.39 - 1.58: 2750 1.58 - 1.77: 0 1.77 - 1.96: 20 1.96 - 2.16: 14 Bond restraints: 4622 Sorted by residual: bond pdb=" C CMO D 202 " pdb=" O CMO D 202 " ideal model delta sigma weight residual 1.141 1.276 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C CMO B 202 " pdb=" O CMO B 202 " ideal model delta sigma weight residual 1.141 1.276 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " ideal model delta sigma weight residual 1.544 1.413 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " ideal model delta sigma weight residual 1.544 1.413 0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C3C HEM C 201 " pdb=" CAC HEM C 201 " ideal model delta sigma weight residual 1.544 1.442 0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 4617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4864 1.95 - 3.91: 1194 3.91 - 5.86: 234 5.86 - 7.81: 32 7.81 - 9.77: 14 Bond angle restraints: 6338 Sorted by residual: angle pdb=" CA HIS B 97 " pdb=" CB HIS B 97 " pdb=" CG HIS B 97 " ideal model delta sigma weight residual 113.80 104.47 9.33 1.00e+00 1.00e+00 8.70e+01 angle pdb=" CA HIS D 97 " pdb=" CB HIS D 97 " pdb=" CG HIS D 97 " ideal model delta sigma weight residual 113.80 104.47 9.33 1.00e+00 1.00e+00 8.70e+01 angle pdb=" CA PHE C 43 " pdb=" CB PHE C 43 " pdb=" CG PHE C 43 " ideal model delta sigma weight residual 113.80 121.15 -7.35 1.00e+00 1.00e+00 5.40e+01 angle pdb=" CA PHE A 43 " pdb=" CB PHE A 43 " pdb=" CG PHE A 43 " ideal model delta sigma weight residual 113.80 121.15 -7.35 1.00e+00 1.00e+00 5.40e+01 angle pdb=" N LEU D 88 " pdb=" CA LEU D 88 " pdb=" CB LEU D 88 " ideal model delta sigma weight residual 110.28 100.51 9.77 1.55e+00 4.16e-01 3.97e+01 ... (remaining 6333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 2324 17.15 - 34.31: 196 34.31 - 51.46: 68 51.46 - 68.61: 20 68.61 - 85.76: 14 Dihedral angle restraints: 2622 sinusoidal: 998 harmonic: 1624 Sorted by residual: dihedral pdb=" CD ARG B 104 " pdb=" NE ARG B 104 " pdb=" CZ ARG B 104 " pdb=" NH1 ARG B 104 " ideal model delta sinusoidal sigma weight residual 0.00 -42.15 42.15 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CD ARG D 104 " pdb=" NE ARG D 104 " pdb=" CZ ARG D 104 " pdb=" NH1 ARG D 104 " ideal model delta sinusoidal sigma weight residual 0.00 -42.15 42.15 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -40.29 40.29 2 1.00e+01 1.00e-02 2.01e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 342 0.056 - 0.113: 212 0.113 - 0.169: 78 0.169 - 0.225: 38 0.225 - 0.281: 20 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA HIS D 143 " pdb=" N HIS D 143 " pdb=" C HIS D 143 " pdb=" CB HIS D 143 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA HIS B 143 " pdb=" N HIS B 143 " pdb=" C HIS B 143 " pdb=" CB HIS B 143 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA PHE D 118 " pdb=" N PHE D 118 " pdb=" C PHE D 118 " pdb=" CB PHE D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 687 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 104 " 0.859 9.50e-02 1.11e+02 3.86e-01 1.00e+02 pdb=" NE ARG D 104 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG D 104 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG D 104 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 104 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 104 " -0.859 9.50e-02 1.11e+02 3.86e-01 1.00e+02 pdb=" NE ARG B 104 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG B 104 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG B 104 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 104 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 30 " -0.586 9.50e-02 1.11e+02 2.63e-01 4.25e+01 pdb=" NE ARG B 30 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 30 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 30 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 30 " -0.021 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1348 2.87 - 3.38: 4324 3.38 - 3.88: 8136 3.88 - 4.39: 9110 4.39 - 4.90: 14790 Nonbonded interactions: 37708 Sorted by model distance: nonbonded pdb=" OD2 ASP C 85 " pdb=" NH1 ARG C 141 " model vdw 2.360 3.120 nonbonded pdb=" OD2 ASP A 85 " pdb=" NH1 ARG A 141 " model vdw 2.360 3.120 nonbonded pdb=" NE2 HIS A 103 " pdb=" OE1 GLN B 131 " model vdw 2.490 3.120 nonbonded pdb=" NE2 HIS C 103 " pdb=" OE1 GLN D 131 " model vdw 2.490 3.120 nonbonded pdb=" OD1 ASP B 21 " pdb=" NZ LYS B 65 " model vdw 2.521 3.120 ... (remaining 37703 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.740 Find NCS groups from input model: 0.020 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:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.015 0.187 4626 Z= 0.834 Angle : 1.796 9.766 6338 Z= 1.202 Chirality : 0.094 0.281 690 Planarity : 0.027 0.386 792 Dihedral : 17.072 85.757 1570 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.79 % Favored : 97.85 % Rotamer: Outliers : 5.29 % Allowed : 7.49 % Favored : 87.22 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.32), residues: 558 helix: -0.81 (0.22), residues: 420 sheet: None (None), residues: 0 loop : 0.07 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.008 ARG D 104 TYR 0.028 0.013 TYR B 130 PHE 0.049 0.010 PHE C 36 TRP 0.033 0.010 TRP C 14 HIS 0.034 0.006 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.01457 ( 4622) covalent geometry : angle 1.79569 ( 6338) hydrogen bonds : bond 0.24690 ( 336) hydrogen bonds : angle 6.78369 ( 954) Misc. bond : bond 0.17269 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.087 Fit side-chains REVERT: A 92 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: A 116 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 141 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6416 (tmm160) REVERT: B 61 LYS cc_start: 0.8034 (tttt) cc_final: 0.7077 (mttt) REVERT: B 66 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8124 (mtpp) REVERT: B 139 ASN cc_start: 0.7527 (m-40) cc_final: 0.7291 (m-40) REVERT: C 92 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: C 116 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: C 141 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6416 (tmm160) REVERT: D 61 LYS cc_start: 0.8035 (tttt) cc_final: 0.7078 (mttt) REVERT: D 66 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8128 (mtpp) REVERT: D 139 ASN cc_start: 0.7524 (m-40) cc_final: 0.7289 (m-40) outliers start: 24 outliers final: 4 residues processed: 122 average time/residue: 0.3763 time to fit residues: 47.3046 Evaluate side-chains 110 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113380 restraints weight = 3901.065| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.20 r_work: 0.3071 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4626 Z= 0.146 Angle : 0.645 5.410 6338 Z= 0.316 Chirality : 0.040 0.123 690 Planarity : 0.006 0.062 792 Dihedral : 13.193 88.751 648 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.37), residues: 558 helix: 2.08 (0.25), residues: 418 sheet: None (None), residues: 0 loop : 1.13 (0.64), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.008 0.002 TYR D 35 PHE 0.014 0.002 PHE C 43 TRP 0.011 0.001 TRP C 14 HIS 0.024 0.002 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4622) covalent geometry : angle 0.64473 ( 6338) hydrogen bonds : bond 0.04998 ( 336) hydrogen bonds : angle 4.24378 ( 954) Misc. bond : bond 0.04083 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.089 Fit side-chains REVERT: A 56 LYS cc_start: 0.8481 (tttp) cc_final: 0.7671 (mmtm) REVERT: A 141 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6518 (tmm160) REVERT: B 61 LYS cc_start: 0.8315 (tttt) cc_final: 0.7590 (mttm) REVERT: B 66 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8179 (mtpp) REVERT: B 97 HIS cc_start: 0.6763 (t70) cc_final: 0.5828 (m90) REVERT: C 56 LYS cc_start: 0.8482 (tttp) cc_final: 0.7674 (mmtm) REVERT: C 141 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6518 (tmm160) REVERT: D 61 LYS cc_start: 0.8327 (tttt) cc_final: 0.7601 (mttm) REVERT: D 66 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8186 (mtpp) REVERT: D 97 HIS cc_start: 0.6762 (t70) cc_final: 0.5824 (m90) outliers start: 12 outliers final: 0 residues processed: 110 average time/residue: 0.3524 time to fit residues: 40.0567 Evaluate side-chains 98 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain C residue 141 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** D 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121438 restraints weight = 3879.001| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 0.99 r_work: 0.3136 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4626 Z= 0.145 Angle : 0.618 5.252 6338 Z= 0.299 Chirality : 0.040 0.122 690 Planarity : 0.006 0.053 792 Dihedral : 11.612 89.790 626 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.20 % Allowed : 15.86 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.38), residues: 558 helix: 2.53 (0.25), residues: 432 sheet: None (None), residues: 0 loop : 1.58 (0.70), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.008 0.002 TYR B 35 PHE 0.012 0.001 PHE A 43 TRP 0.009 0.001 TRP C 14 HIS 0.017 0.002 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4622) covalent geometry : angle 0.61844 ( 6338) hydrogen bonds : bond 0.05003 ( 336) hydrogen bonds : angle 4.06028 ( 954) Misc. bond : bond 0.04153 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.091 Fit side-chains REVERT: A 56 LYS cc_start: 0.8545 (tttp) cc_final: 0.8037 (mmtm) REVERT: B 61 LYS cc_start: 0.8453 (tttt) cc_final: 0.7843 (mttt) REVERT: B 66 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8233 (mtpp) REVERT: B 97 HIS cc_start: 0.7033 (t70) cc_final: 0.6169 (m90) REVERT: C 56 LYS cc_start: 0.8549 (tttp) cc_final: 0.8030 (mmtm) REVERT: D 61 LYS cc_start: 0.8461 (tttt) cc_final: 0.7836 (mttt) REVERT: D 66 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8237 (mtpp) REVERT: D 97 HIS cc_start: 0.7029 (t70) cc_final: 0.6165 (m90) outliers start: 10 outliers final: 2 residues processed: 98 average time/residue: 0.3514 time to fit residues: 35.6037 Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain D residue 55 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS D 97 HIS D 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.138785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119593 restraints weight = 3880.674| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 0.94 r_work: 0.3119 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4626 Z= 0.181 Angle : 0.665 5.573 6338 Z= 0.326 Chirality : 0.043 0.146 690 Planarity : 0.006 0.059 792 Dihedral : 11.815 88.838 618 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.37), residues: 558 helix: 2.42 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.56 (0.69), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.007 0.002 TYR B 35 PHE 0.014 0.002 PHE A 43 TRP 0.008 0.001 TRP A 14 HIS 0.017 0.002 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 4622) covalent geometry : angle 0.66483 ( 6338) hydrogen bonds : bond 0.05911 ( 336) hydrogen bonds : angle 4.17347 ( 954) Misc. bond : bond 0.04410 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.094 Fit side-chains REVERT: B 61 LYS cc_start: 0.8514 (tttt) cc_final: 0.7893 (mttm) REVERT: B 66 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8247 (mtpp) REVERT: B 97 HIS cc_start: 0.6845 (t-90) cc_final: 0.6287 (m90) REVERT: D 61 LYS cc_start: 0.8514 (tttt) cc_final: 0.7879 (mttm) REVERT: D 66 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8246 (mtpp) REVERT: D 97 HIS cc_start: 0.6844 (t-90) cc_final: 0.6286 (m90) outliers start: 12 outliers final: 2 residues processed: 94 average time/residue: 0.3583 time to fit residues: 34.8519 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122629 restraints weight = 3865.698| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.93 r_work: 0.3162 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4626 Z= 0.131 Angle : 0.582 5.127 6338 Z= 0.278 Chirality : 0.039 0.119 690 Planarity : 0.005 0.046 792 Dihedral : 11.211 88.917 618 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.88 % Allowed : 15.42 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.38), residues: 558 helix: 2.69 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.72 (0.72), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 104 TYR 0.006 0.001 TYR D 35 PHE 0.011 0.001 PHE A 43 TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4622) covalent geometry : angle 0.58180 ( 6338) hydrogen bonds : bond 0.04446 ( 336) hydrogen bonds : angle 3.93287 ( 954) Misc. bond : bond 0.04191 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.088 Fit side-chains REVERT: A 56 LYS cc_start: 0.8530 (tttp) cc_final: 0.8016 (mmtm) REVERT: A 76 MET cc_start: 0.8909 (mtp) cc_final: 0.8536 (mtm) REVERT: B 61 LYS cc_start: 0.8486 (tttt) cc_final: 0.7880 (mttt) REVERT: B 66 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8282 (mtpp) REVERT: B 97 HIS cc_start: 0.6890 (t-90) cc_final: 0.6162 (m90) REVERT: C 56 LYS cc_start: 0.8532 (tttp) cc_final: 0.8017 (mmtm) REVERT: C 76 MET cc_start: 0.8905 (mtp) cc_final: 0.8529 (mtm) REVERT: D 61 LYS cc_start: 0.8489 (tttt) cc_final: 0.7871 (mttt) REVERT: D 66 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8279 (mtpp) REVERT: D 97 HIS cc_start: 0.6889 (t-90) cc_final: 0.6159 (m90) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.3374 time to fit residues: 33.5401 Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.133142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110314 restraints weight = 3982.803| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.27 r_work: 0.3025 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4626 Z= 0.170 Angle : 0.642 5.621 6338 Z= 0.311 Chirality : 0.042 0.130 690 Planarity : 0.006 0.046 792 Dihedral : 11.509 89.231 618 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.88 % Allowed : 15.20 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.37), residues: 558 helix: 2.58 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.70 (0.70), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 104 TYR 0.006 0.002 TYR B 35 PHE 0.013 0.002 PHE A 43 TRP 0.007 0.001 TRP A 14 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 4622) covalent geometry : angle 0.64222 ( 6338) hydrogen bonds : bond 0.05624 ( 336) hydrogen bonds : angle 4.08735 ( 954) Misc. bond : bond 0.04359 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.103 Fit side-chains REVERT: A 56 LYS cc_start: 0.8401 (tttp) cc_final: 0.7537 (mmtm) REVERT: A 76 MET cc_start: 0.8908 (mtp) cc_final: 0.8678 (mtm) REVERT: B 61 LYS cc_start: 0.8305 (tttt) cc_final: 0.7472 (mttm) REVERT: B 66 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8097 (mtpp) REVERT: B 97 HIS cc_start: 0.6997 (t-90) cc_final: 0.5988 (m90) REVERT: C 56 LYS cc_start: 0.8402 (tttp) cc_final: 0.7541 (mmtm) REVERT: C 76 MET cc_start: 0.8908 (mtp) cc_final: 0.8678 (mtm) REVERT: D 61 LYS cc_start: 0.8301 (tttt) cc_final: 0.7468 (mttm) REVERT: D 66 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8102 (mtpp) REVERT: D 97 HIS cc_start: 0.7004 (t-90) cc_final: 0.5998 (m90) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.3797 time to fit residues: 35.3901 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112846 restraints weight = 3957.383| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.23 r_work: 0.3064 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4626 Z= 0.135 Angle : 0.585 5.301 6338 Z= 0.278 Chirality : 0.039 0.120 690 Planarity : 0.005 0.045 792 Dihedral : 11.040 89.017 618 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.88 % Allowed : 15.64 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.37), residues: 558 helix: 2.73 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.75 (0.72), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 104 TYR 0.006 0.001 TYR D 130 PHE 0.011 0.001 PHE A 43 TRP 0.008 0.001 TRP A 14 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4622) covalent geometry : angle 0.58541 ( 6338) hydrogen bonds : bond 0.04563 ( 336) hydrogen bonds : angle 3.93623 ( 954) Misc. bond : bond 0.04160 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.165 Fit side-chains REVERT: A 56 LYS cc_start: 0.8456 (tttp) cc_final: 0.7727 (mmtm) REVERT: A 76 MET cc_start: 0.8881 (mtp) cc_final: 0.8610 (mtm) REVERT: B 61 LYS cc_start: 0.8354 (tttt) cc_final: 0.7558 (mttm) REVERT: B 66 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8155 (mtpp) REVERT: B 97 HIS cc_start: 0.6727 (t-90) cc_final: 0.5933 (m90) REVERT: C 56 LYS cc_start: 0.8461 (tttp) cc_final: 0.7735 (mmtm) REVERT: C 76 MET cc_start: 0.8883 (mtp) cc_final: 0.8613 (mtm) REVERT: D 61 LYS cc_start: 0.8354 (tttt) cc_final: 0.7560 (mttm) REVERT: D 66 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8158 (mtpp) REVERT: D 97 HIS cc_start: 0.6730 (t-90) cc_final: 0.5941 (m90) outliers start: 4 outliers final: 2 residues processed: 92 average time/residue: 0.3779 time to fit residues: 35.9146 Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 HIS D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110539 restraints weight = 3922.088| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.21 r_work: 0.3034 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4626 Z= 0.171 Angle : 0.641 5.704 6338 Z= 0.309 Chirality : 0.042 0.131 690 Planarity : 0.006 0.046 792 Dihedral : 11.413 89.237 618 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.32 % Allowed : 15.42 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.37), residues: 558 helix: 2.60 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.66 (0.69), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.006 0.002 TYR B 35 PHE 0.012 0.002 PHE C 43 TRP 0.007 0.001 TRP C 14 HIS 0.008 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4622) covalent geometry : angle 0.64131 ( 6338) hydrogen bonds : bond 0.05664 ( 336) hydrogen bonds : angle 4.09073 ( 954) Misc. bond : bond 0.04078 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.090 Fit side-chains REVERT: A 56 LYS cc_start: 0.8406 (tttp) cc_final: 0.7578 (mmtm) REVERT: A 76 MET cc_start: 0.8892 (mtp) cc_final: 0.8670 (mtm) REVERT: B 61 LYS cc_start: 0.8322 (tttt) cc_final: 0.7512 (mttm) REVERT: B 66 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8139 (mtpp) REVERT: B 97 HIS cc_start: 0.6941 (t-90) cc_final: 0.6021 (m90) REVERT: B 101 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: B 104 ARG cc_start: 0.8499 (ttt-90) cc_final: 0.8130 (ttp-110) REVERT: C 56 LYS cc_start: 0.8411 (tttp) cc_final: 0.7584 (mmtm) REVERT: C 76 MET cc_start: 0.8891 (mtp) cc_final: 0.8666 (mtm) REVERT: D 61 LYS cc_start: 0.8319 (tttt) cc_final: 0.7517 (mttm) REVERT: D 66 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8149 (mtpp) REVERT: D 97 HIS cc_start: 0.6943 (t-90) cc_final: 0.6026 (m90) REVERT: D 101 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: D 104 ARG cc_start: 0.8498 (ttt-90) cc_final: 0.8127 (ttp-110) outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.3648 time to fit residues: 33.1820 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 32 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.114334 restraints weight = 3944.915| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.22 r_work: 0.3082 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4626 Z= 0.119 Angle : 0.555 5.124 6338 Z= 0.262 Chirality : 0.038 0.119 690 Planarity : 0.005 0.045 792 Dihedral : 10.698 89.011 618 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.10 % Allowed : 15.64 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.37), residues: 558 helix: 2.85 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.79 (0.72), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.006 0.001 TYR D 130 PHE 0.009 0.001 PHE C 43 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4622) covalent geometry : angle 0.55542 ( 6338) hydrogen bonds : bond 0.03958 ( 336) hydrogen bonds : angle 3.85301 ( 954) Misc. bond : bond 0.03787 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.104 Fit side-chains REVERT: A 56 LYS cc_start: 0.8388 (tttp) cc_final: 0.7648 (mmtm) REVERT: A 76 MET cc_start: 0.8816 (mtp) cc_final: 0.8556 (mtm) REVERT: B 61 LYS cc_start: 0.8252 (tttt) cc_final: 0.7463 (mttt) REVERT: B 66 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8083 (mtpp) REVERT: B 97 HIS cc_start: 0.6604 (t-90) cc_final: 0.5896 (m90) REVERT: C 56 LYS cc_start: 0.8392 (tttp) cc_final: 0.7655 (mmtm) REVERT: C 76 MET cc_start: 0.8819 (mtp) cc_final: 0.8557 (mtm) REVERT: D 61 LYS cc_start: 0.8254 (tttt) cc_final: 0.7468 (mttt) REVERT: D 66 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8086 (mtpp) REVERT: D 97 HIS cc_start: 0.6606 (t-90) cc_final: 0.5901 (m90) outliers start: 5 outliers final: 1 residues processed: 99 average time/residue: 0.3560 time to fit residues: 36.5241 Evaluate side-chains 91 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119418 restraints weight = 3896.932| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.49 r_work: 0.3086 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4626 Z= 0.140 Angle : 0.593 5.265 6338 Z= 0.281 Chirality : 0.040 0.124 690 Planarity : 0.005 0.045 792 Dihedral : 10.953 89.081 618 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.44 % Allowed : 15.42 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.37), residues: 558 helix: 2.77 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.71 (0.71), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.006 0.001 TYR D 130 PHE 0.012 0.001 PHE C 43 TRP 0.007 0.001 TRP C 14 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4622) covalent geometry : angle 0.59306 ( 6338) hydrogen bonds : bond 0.04773 ( 336) hydrogen bonds : angle 3.95822 ( 954) Misc. bond : bond 0.03930 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.090 Fit side-chains REVERT: A 56 LYS cc_start: 0.8625 (tttp) cc_final: 0.8075 (mmtm) REVERT: B 61 LYS cc_start: 0.8548 (tttt) cc_final: 0.7929 (mttt) REVERT: B 66 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8410 (mtpp) REVERT: B 97 HIS cc_start: 0.6840 (t-90) cc_final: 0.6112 (m90) REVERT: C 56 LYS cc_start: 0.8634 (tttp) cc_final: 0.8084 (mmtm) REVERT: D 61 LYS cc_start: 0.8550 (tttt) cc_final: 0.7930 (mttt) REVERT: D 66 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8420 (mtpp) REVERT: D 97 HIS cc_start: 0.6857 (t-90) cc_final: 0.6133 (m90) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.3576 time to fit residues: 33.2578 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.0050 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 51 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122116 restraints weight = 3928.772| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.47 r_work: 0.3129 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4626 Z= 0.115 Angle : 0.550 5.137 6338 Z= 0.257 Chirality : 0.038 0.118 690 Planarity : 0.005 0.045 792 Dihedral : 10.492 88.884 618 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.44 % Allowed : 14.98 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.37), residues: 558 helix: 2.94 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.74 (0.71), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 30 TYR 0.006 0.001 TYR B 130 PHE 0.009 0.001 PHE C 43 TRP 0.008 0.001 TRP C 14 HIS 0.002 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4622) covalent geometry : angle 0.54988 ( 6338) hydrogen bonds : bond 0.03742 ( 336) hydrogen bonds : angle 3.81435 ( 954) Misc. bond : bond 0.03529 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1188.84 seconds wall clock time: 30 minutes 56.35 seconds (1856.35 seconds total)