Starting phenix.real_space_refine on Fri Aug 22 15:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_65082.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_65082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_65082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_65082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vib_65082/08_2025/9vib_65082.map" } 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-2.0-5787/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: 1.33, per 1000 atoms: 0.30 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: 0.36 Conformation dependent library (CDL) restraints added in 185.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.66 Time building geometry restraints manager: 0.52 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=" 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 bond pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " ideal model delta sigma weight residual 1.544 1.442 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C3A HEM C 201 " pdb=" C4A HEM C 201 " ideal model delta sigma weight residual 1.449 1.367 0.082 2.00e-02 2.50e+03 1.68e+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 - 3.06: 2594 3.06 - 3.76: 8520 3.76 - 4.46: 13696 4.46 - 5.16: 21124 5.16 - 5.86: 25106 Nonbonded interactions: 71040 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 71035 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: 0.01 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: 1.450 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- 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= 0.818 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 aren 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 0.01421 ( 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 : 0.168 Fit side-chains REVERT: A 92 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7689 (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 30 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7548 (mtt90) REVERT: B 61 LYS cc_start: 0.8034 (tttt) cc_final: 0.7075 (mttt) REVERT: B 66 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8125 (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 30 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7544 (mtt90) REVERT: D 61 LYS cc_start: 0.8035 (tttt) cc_final: 0.7077 (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: 0.7288 (m-40) outliers start: 24 outliers final: 4 residues processed: 122 average time/residue: 0.6149 time to fit residues: 77.3667 Evaluate side-chains 112 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 B residue 30 ARG 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 Chi-restraints excluded: chain D residue 30 ARG 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: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 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 58 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 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 = 0.3503 r_free = 0.3503 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115151 restraints weight = 3879.527| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.20 r_work: 0.3103 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.143 Angle : 0.651 5.484 6338 Z= 0.314 Chirality : 0.040 0.124 690 Planarity : 0.005 0.039 792 Dihedral : 13.053 88.048 656 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.20 % Allowed : 13.22 % 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 aren not related in a simple way. whole: 2.63 (0.37), residues: 558 helix: 2.03 (0.25), residues: 420 sheet: None (None), residues: 0 loop : 1.04 (0.65), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 31 TYR 0.007 0.002 TYR B 35 PHE 0.013 0.002 PHE C 43 TRP 0.011 0.001 TRP C 14 HIS 0.023 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4622) covalent geometry : angle 0.65117 ( 6338) hydrogen bonds : bond 0.04731 ( 336) hydrogen bonds : angle 4.20770 ( 954) Misc. bond : bond 0.00467 ( 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 114 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.173 Fit side-chains REVERT: A 56 LYS cc_start: 0.8458 (tttp) cc_final: 0.7650 (mmtm) REVERT: A 141 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6458 (tmm160) REVERT: B 3 LEU cc_start: 0.7893 (mp) cc_final: 0.7677 (mt) REVERT: B 61 LYS cc_start: 0.8322 (tttt) cc_final: 0.7602 (mttt) REVERT: B 66 LYS cc_start: 0.8324 (mtmt) cc_final: 0.8048 (mtpt) REVERT: B 97 HIS cc_start: 0.6786 (t70) cc_final: 0.5853 (m90) REVERT: C 56 LYS cc_start: 0.8462 (tttp) cc_final: 0.7660 (mmtm) REVERT: C 141 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6457 (tmm160) REVERT: D 3 LEU cc_start: 0.7898 (mp) cc_final: 0.7683 (mt) REVERT: D 61 LYS cc_start: 0.8331 (tttt) cc_final: 0.7611 (mttt) REVERT: D 66 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8052 (mtpt) REVERT: D 97 HIS cc_start: 0.6784 (t70) cc_final: 0.5847 (m90) outliers start: 10 outliers final: 0 residues processed: 110 average time/residue: 0.5854 time to fit residues: 66.6617 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 : 0.179 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120204 restraints weight = 3882.007| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.32 r_work: 0.3132 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4626 Z= 0.164 Angle : 0.656 5.350 6338 Z= 0.319 Chirality : 0.042 0.133 690 Planarity : 0.005 0.043 792 Dihedral : 11.718 88.890 626 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.20 % Allowed : 13.66 % 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 aren not related in a simple way. whole: 3.20 (0.37), residues: 558 helix: 2.37 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.41 (0.69), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 31 TYR 0.008 0.002 TYR D 35 PHE 0.013 0.002 PHE C 43 TRP 0.009 0.001 TRP A 14 HIS 0.018 0.002 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4622) covalent geometry : angle 0.65629 ( 6338) hydrogen bonds : bond 0.05523 ( 336) hydrogen bonds : angle 4.14336 ( 954) Misc. bond : bond 0.02928 ( 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 102 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.209 Fit side-chains REVERT: B 3 LEU cc_start: 0.7860 (mp) cc_final: 0.7625 (mt) REVERT: B 61 LYS cc_start: 0.8524 (tttt) cc_final: 0.7933 (mttm) REVERT: B 66 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8271 (mtpp) REVERT: B 97 HIS cc_start: 0.7146 (t70) cc_final: 0.6191 (m90) REVERT: B 101 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: D 3 LEU cc_start: 0.7861 (mp) cc_final: 0.7624 (mt) REVERT: D 61 LYS cc_start: 0.8520 (tttt) cc_final: 0.7923 (mttm) REVERT: D 66 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8270 (mtpp) REVERT: D 97 HIS cc_start: 0.7151 (t70) cc_final: 0.6197 (m90) REVERT: D 101 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7520 (tm-30) outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 0.5872 time to fit residues: 58.2892 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 : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.138211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115966 restraints weight = 3893.165| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.22 r_work: 0.3109 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4626 Z= 0.121 Angle : 0.575 5.245 6338 Z= 0.270 Chirality : 0.038 0.117 690 Planarity : 0.005 0.045 792 Dihedral : 10.727 88.713 618 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.76 % Allowed : 14.98 % 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 aren not related in a simple way. whole: 3.73 (0.38), residues: 558 helix: 2.71 (0.25), residues: 434 sheet: None (None), residues: 0 loop : 1.72 (0.73), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 31 TYR 0.006 0.001 TYR B 35 PHE 0.010 0.001 PHE A 43 TRP 0.009 0.001 TRP A 14 HIS 0.014 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4622) covalent geometry : angle 0.57505 ( 6338) hydrogen bonds : bond 0.03997 ( 336) hydrogen bonds : angle 3.87063 ( 954) Misc. bond : bond 0.01235 ( 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 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.112 Fit side-chains REVERT: A 56 LYS cc_start: 0.8395 (tttp) cc_final: 0.7629 (mmtm) REVERT: A 76 MET cc_start: 0.8808 (mtp) cc_final: 0.8580 (mtm) REVERT: B 3 LEU cc_start: 0.7813 (mp) cc_final: 0.7566 (mt) REVERT: B 61 LYS cc_start: 0.8264 (tttt) cc_final: 0.7510 (mttt) REVERT: B 66 LYS cc_start: 0.8324 (mtmt) cc_final: 0.8032 (mtpp) REVERT: B 97 HIS cc_start: 0.6533 (t-90) cc_final: 0.6055 (m90) REVERT: C 56 LYS cc_start: 0.8393 (tttp) cc_final: 0.7624 (mmtm) REVERT: C 76 MET cc_start: 0.8811 (mtp) cc_final: 0.8582 (mtm) REVERT: D 3 LEU cc_start: 0.7817 (mp) cc_final: 0.7572 (mt) REVERT: D 61 LYS cc_start: 0.8266 (tttt) cc_final: 0.7511 (mttt) REVERT: D 66 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8036 (mtpp) REVERT: D 97 HIS cc_start: 0.6540 (t-90) cc_final: 0.6062 (m90) outliers start: 8 outliers final: 2 residues processed: 98 average time/residue: 0.5308 time to fit residues: 53.8366 Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain C residue 16 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS B 139 ASN D 63 HIS D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123542 restraints weight = 3850.920| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.92 r_work: 0.3185 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4626 Z= 0.136 Angle : 0.598 5.155 6338 Z= 0.283 Chirality : 0.040 0.120 690 Planarity : 0.005 0.045 792 Dihedral : 10.627 88.874 618 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 : 1.76 % Allowed : 15.42 % Favored : 82.82 % 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 aren not related in a simple way. whole: 3.72 (0.38), residues: 558 helix: 2.74 (0.25), residues: 432 sheet: None (None), residues: 0 loop : 1.56 (0.71), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.007 0.001 TYR D 35 PHE 0.011 0.001 PHE C 43 TRP 0.008 0.001 TRP A 14 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4622) covalent geometry : angle 0.59841 ( 6338) hydrogen bonds : bond 0.04683 ( 336) hydrogen bonds : angle 3.93634 ( 954) Misc. bond : bond 0.02394 ( 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 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.156 Fit side-chains REVERT: A 56 LYS cc_start: 0.8544 (tttp) cc_final: 0.8001 (mmtm) REVERT: B 3 LEU cc_start: 0.7861 (mp) cc_final: 0.7629 (mt) REVERT: B 61 LYS cc_start: 0.8489 (tttt) cc_final: 0.7885 (mttt) REVERT: B 66 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8259 (mtpp) REVERT: B 97 HIS cc_start: 0.6847 (t-90) cc_final: 0.6168 (m90) REVERT: B 101 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: C 56 LYS cc_start: 0.8547 (tttp) cc_final: 0.7995 (mmtm) REVERT: D 3 LEU cc_start: 0.7871 (mp) cc_final: 0.7634 (mt) REVERT: D 61 LYS cc_start: 0.8490 (tttt) cc_final: 0.7875 (mttt) REVERT: D 66 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8253 (mtpp) REVERT: D 97 HIS cc_start: 0.6850 (t-90) cc_final: 0.6170 (m90) REVERT: D 101 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7315 (tm-30) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.4932 time to fit residues: 51.1338 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 : 0.106 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112788 restraints weight = 3986.071| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.25 r_work: 0.3068 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.145 Angle : 0.612 5.258 6338 Z= 0.291 Chirality : 0.041 0.121 690 Planarity : 0.005 0.046 792 Dihedral : 10.917 89.121 618 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 : 0.88 % Allowed : 16.30 % Favored : 82.82 % 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 aren not related in a simple way. whole: 3.67 (0.37), residues: 558 helix: 2.71 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.54 (0.71), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.006 0.001 TYR D 35 PHE 0.012 0.002 PHE C 43 TRP 0.008 0.001 TRP C 14 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4622) covalent geometry : angle 0.61202 ( 6338) hydrogen bonds : bond 0.04886 ( 336) hydrogen bonds : angle 3.96812 ( 954) Misc. bond : bond 0.03237 ( 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 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.101 Fit side-chains REVERT: A 56 LYS cc_start: 0.8411 (tttp) cc_final: 0.7561 (mmtm) REVERT: B 3 LEU cc_start: 0.7818 (mp) cc_final: 0.7530 (mt) REVERT: B 61 LYS cc_start: 0.8281 (tttt) cc_final: 0.7459 (mttt) REVERT: B 66 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8055 (mtpp) REVERT: B 97 HIS cc_start: 0.6797 (t-90) cc_final: 0.5961 (m90) REVERT: C 56 LYS cc_start: 0.8418 (tttp) cc_final: 0.7568 (mmtm) REVERT: D 3 LEU cc_start: 0.7822 (mp) cc_final: 0.7531 (mt) REVERT: D 61 LYS cc_start: 0.8281 (tttt) cc_final: 0.7460 (mttt) REVERT: D 66 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8057 (mtpp) REVERT: D 97 HIS cc_start: 0.6803 (t-90) cc_final: 0.5964 (m90) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.5205 time to fit residues: 50.6115 Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.136670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114142 restraints weight = 3969.041| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.25 r_work: 0.3083 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4626 Z= 0.131 Angle : 0.587 5.150 6338 Z= 0.276 Chirality : 0.039 0.120 690 Planarity : 0.005 0.045 792 Dihedral : 10.666 89.180 618 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.76 % Allowed : 14.98 % 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 aren not related in a simple way. whole: 3.81 (0.37), residues: 558 helix: 2.80 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.66 (0.72), residues: 126 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 A 14 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4622) covalent geometry : angle 0.58666 ( 6338) hydrogen bonds : bond 0.04389 ( 336) hydrogen bonds : angle 3.89538 ( 954) Misc. bond : bond 0.02309 ( 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 106 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.124 Fit side-chains REVERT: A 56 LYS cc_start: 0.8387 (tttp) cc_final: 0.7574 (mmtm) REVERT: B 3 LEU cc_start: 0.7817 (mp) cc_final: 0.7536 (mt) REVERT: B 61 LYS cc_start: 0.8304 (tttt) cc_final: 0.7489 (mttt) REVERT: B 66 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8074 (mtpp) REVERT: B 97 HIS cc_start: 0.6575 (t-90) cc_final: 0.5907 (m90) REVERT: C 56 LYS cc_start: 0.8394 (tttp) cc_final: 0.7586 (mmtm) REVERT: D 3 LEU cc_start: 0.7821 (mp) cc_final: 0.7541 (mt) REVERT: D 61 LYS cc_start: 0.8305 (tttt) cc_final: 0.7493 (mttt) REVERT: D 66 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8081 (mtpp) REVERT: D 97 HIS cc_start: 0.6577 (t-90) cc_final: 0.5912 (m90) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.5461 time to fit residues: 57.5892 Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111743 restraints weight = 3927.806| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.24 r_work: 0.3057 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4626 Z= 0.167 Angle : 0.643 5.734 6338 Z= 0.307 Chirality : 0.042 0.124 690 Planarity : 0.005 0.046 792 Dihedral : 11.166 89.316 618 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.37 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 aren not related in a simple way. whole: 3.61 (0.37), residues: 558 helix: 2.66 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 1.60 (0.69), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 104 TYR 0.006 0.002 TYR B 35 PHE 0.012 0.002 PHE C 43 TRP 0.007 0.001 TRP A 14 HIS 0.006 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4622) covalent geometry : angle 0.64256 ( 6338) hydrogen bonds : bond 0.05479 ( 336) hydrogen bonds : angle 4.04968 ( 954) Misc. bond : bond 0.03900 ( 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 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.109 Fit side-chains REVERT: A 56 LYS cc_start: 0.8410 (tttp) cc_final: 0.7548 (mmtm) REVERT: B 3 LEU cc_start: 0.7816 (mp) cc_final: 0.7462 (mt) REVERT: B 61 LYS cc_start: 0.8293 (tttt) cc_final: 0.7472 (mttm) REVERT: B 66 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8112 (mtpt) REVERT: B 97 HIS cc_start: 0.6799 (t-90) cc_final: 0.5964 (m90) REVERT: C 56 LYS cc_start: 0.8422 (tttp) cc_final: 0.7561 (mmtm) REVERT: D 3 LEU cc_start: 0.7826 (mp) cc_final: 0.7469 (mt) REVERT: D 61 LYS cc_start: 0.8296 (tttt) cc_final: 0.7476 (mttm) REVERT: D 66 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8115 (mtpt) REVERT: D 97 HIS cc_start: 0.6801 (t-90) cc_final: 0.5967 (m90) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.5332 time to fit residues: 49.5591 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain D residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113517 restraints weight = 3946.326| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.25 r_work: 0.3076 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.139 Angle : 0.602 5.282 6338 Z= 0.283 Chirality : 0.040 0.120 690 Planarity : 0.005 0.045 792 Dihedral : 10.871 89.382 618 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.88 % Allowed : 15.86 % 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 aren not related in a simple way. whole: 3.71 (0.37), residues: 558 helix: 2.73 (0.24), residues: 432 sheet: None (None), residues: 0 loop : 1.62 (0.71), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 104 TYR 0.005 0.001 TYR D 35 PHE 0.012 0.001 PHE A 43 TRP 0.007 0.001 TRP A 14 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4622) covalent geometry : angle 0.60168 ( 6338) hydrogen bonds : bond 0.04635 ( 336) hydrogen bonds : angle 3.93714 ( 954) Misc. bond : bond 0.02320 ( 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 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.179 Fit side-chains REVERT: A 56 LYS cc_start: 0.8403 (tttp) cc_final: 0.7560 (mmtm) REVERT: B 3 LEU cc_start: 0.7825 (mp) cc_final: 0.7491 (mt) REVERT: B 61 LYS cc_start: 0.8286 (tttt) cc_final: 0.7473 (mttt) REVERT: B 66 LYS cc_start: 0.8357 (mtmt) cc_final: 0.8075 (mtpt) REVERT: B 97 HIS cc_start: 0.6460 (t-90) cc_final: 0.5823 (m90) REVERT: C 56 LYS cc_start: 0.8413 (tttp) cc_final: 0.7574 (mmtm) REVERT: D 3 LEU cc_start: 0.7824 (mp) cc_final: 0.7522 (mt) REVERT: D 61 LYS cc_start: 0.8290 (tttt) cc_final: 0.7475 (mttm) REVERT: D 66 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8080 (mtpt) REVERT: D 97 HIS cc_start: 0.6460 (t-90) cc_final: 0.5827 (m90) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.5713 time to fit residues: 56.5503 Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.135575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113023 restraints weight = 3911.152| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.24 r_work: 0.3074 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.143 Angle : 0.607 5.490 6338 Z= 0.287 Chirality : 0.040 0.121 690 Planarity : 0.005 0.046 792 Dihedral : 10.903 89.971 618 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.44 % Allowed : 16.30 % 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 aren not related in a simple way. whole: 3.69 (0.37), residues: 558 helix: 2.69 (0.24), residues: 434 sheet: None (None), residues: 0 loop : 1.65 (0.72), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.006 0.001 TYR D 35 PHE 0.012 0.001 PHE A 43 TRP 0.007 0.001 TRP A 14 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4622) covalent geometry : angle 0.60660 ( 6338) hydrogen bonds : bond 0.04821 ( 336) hydrogen bonds : angle 3.95530 ( 954) Misc. bond : bond 0.02907 ( 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 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.119 Fit side-chains REVERT: A 56 LYS cc_start: 0.8396 (tttp) cc_final: 0.7546 (mmtm) REVERT: B 3 LEU cc_start: 0.7805 (mp) cc_final: 0.7465 (mt) REVERT: B 61 LYS cc_start: 0.8268 (tttt) cc_final: 0.7442 (mttt) REVERT: B 66 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8067 (mtpt) REVERT: B 97 HIS cc_start: 0.6572 (t-90) cc_final: 0.5872 (m90) REVERT: C 56 LYS cc_start: 0.8400 (tttp) cc_final: 0.7553 (mmtm) REVERT: D 3 LEU cc_start: 0.7808 (mp) cc_final: 0.7463 (mt) REVERT: D 61 LYS cc_start: 0.8272 (tttt) cc_final: 0.7448 (mttt) REVERT: D 66 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8071 (mtpt) REVERT: D 97 HIS cc_start: 0.6569 (t-90) cc_final: 0.5879 (m90) outliers start: 2 outliers final: 2 residues processed: 94 average time/residue: 0.6177 time to fit residues: 59.9261 Evaluate side-chains 93 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.140807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119803 restraints weight = 3929.414| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.46 r_work: 0.3095 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4626 Z= 0.163 Angle : 0.634 5.526 6338 Z= 0.303 Chirality : 0.042 0.122 690 Planarity : 0.005 0.046 792 Dihedral : 11.083 88.901 618 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.71 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 aren not related in a simple way. whole: 3.60 (0.37), residues: 558 helix: 2.65 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 1.58 (0.69), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 104 TYR 0.006 0.001 TYR D 35 PHE 0.012 0.002 PHE C 43 TRP 0.007 0.001 TRP C 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4622) covalent geometry : angle 0.63441 ( 6338) hydrogen bonds : bond 0.05350 ( 336) hydrogen bonds : angle 4.04021 ( 954) Misc. bond : bond 0.04120 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.79 seconds wall clock time: 33 minutes 15.61 seconds (1995.61 seconds total)