Starting phenix.real_space_refine on Tue Aug 4 12:13:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.map" model { file = "/net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w35_43762/08_2026/8w35_43762.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 10 5.16 5 C 1500 2.51 5 N 462 2.21 5 O 605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2611 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 942 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 942 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "C" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 727 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 30} Chain breaks: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.42 Number of scatterers: 2611 At special positions: 0 Unit cell: (69.017, 65.8316, 76.4496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 34 15.00 O 605 8.00 N 462 7.00 C 1500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 73.6 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 73.1% alpha, 1.7% beta 12 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 43 through 69 removed outlier: 3.534A pdb=" N GLU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.656A pdb=" N ASP A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 removed outlier: 3.699A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 28 through 38 Processing helix chain 'B' and resid 43 through 69 removed outlier: 3.760A pdb=" N GLU B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.585A pdb=" N ASP B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 76 116 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.29 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 611 1.34 - 1.46: 745 1.46 - 1.57: 1287 1.57 - 1.69: 66 1.69 - 1.81: 20 Bond restraints: 2729 Sorted by residual: bond pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 1.397 1.424 -0.027 1.00e-02 1.00e+04 7.06e+00 bond pdb=" N1 C C 27 " pdb=" C2 C C 27 " ideal model delta sigma weight residual 1.397 1.422 -0.025 1.00e-02 1.00e+04 6.22e+00 bond pdb=" N1 C C 3 " pdb=" C2 C C 3 " ideal model delta sigma weight residual 1.397 1.421 -0.024 1.00e-02 1.00e+04 5.92e+00 bond pdb=" N9 A C 10 " pdb=" C4 A C 10 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.45e+00 bond pdb=" N9 A C 21 " pdb=" C4 A C 21 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.43e+00 ... (remaining 2724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 3556 1.86 - 3.71: 266 3.71 - 5.57: 26 5.57 - 7.43: 3 7.43 - 9.29: 1 Bond angle restraints: 3852 Sorted by residual: angle pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sigma weight residual 118.80 124.07 -5.27 1.10e+00 8.26e-01 2.29e+01 angle pdb=" C2 C C 8 " pdb=" N1 C C 8 " pdb=" C6 C C 8 " ideal model delta sigma weight residual 120.30 118.43 1.87 4.00e-01 6.25e+00 2.18e+01 angle pdb=" C1' C C 27 " pdb=" N1 C C 27 " pdb=" C2 C C 27 " ideal model delta sigma weight residual 118.80 123.89 -5.09 1.10e+00 8.26e-01 2.14e+01 angle pdb=" N1 C C 25 " pdb=" C2 C C 25 " pdb=" O2 C C 25 " ideal model delta sigma weight residual 118.90 121.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N1 C C 27 " pdb=" C2 C C 27 " pdb=" O2 C C 27 " ideal model delta sigma weight residual 118.90 121.67 -2.77 6.00e-01 2.78e+00 2.12e+01 ... (remaining 3847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 1448 18.16 - 36.33: 148 36.33 - 54.49: 56 54.49 - 72.66: 41 72.66 - 90.82: 11 Dihedral angle restraints: 1704 sinusoidal: 1014 harmonic: 690 Sorted by residual: dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 -90.82 90.82 1 3.00e+01 1.11e-03 1.08e+01 dihedral pdb=" C ASN A 93 " pdb=" N ASN A 93 " pdb=" CA ASN A 93 " pdb=" CB ASN A 93 " ideal model delta harmonic sigma weight residual -122.60 -130.55 7.95 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" CB LYS B 75 " pdb=" CG LYS B 75 " pdb=" CD LYS B 75 " pdb=" CE LYS B 75 " ideal model delta sinusoidal sigma weight residual 60.00 118.22 -58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 259 0.036 - 0.071: 100 0.071 - 0.106: 46 0.106 - 0.142: 40 0.142 - 0.177: 5 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA ASN A 93 " pdb=" N ASN A 93 " pdb=" C ASN A 93 " pdb=" CB ASN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL B 94 " pdb=" CA VAL B 94 " pdb=" CG1 VAL B 94 " pdb=" CG2 VAL B 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA TYR B 107 " pdb=" N TYR B 107 " pdb=" C TYR B 107 " pdb=" CB TYR B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 447 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 89 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 90 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 90 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 109 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C THR A 109 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 109 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 110 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 73 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 74 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.023 5.00e-02 4.00e+02 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 795 2.86 - 3.37: 2176 3.37 - 3.88: 4491 3.88 - 4.39: 5203 4.39 - 4.90: 7944 Nonbonded interactions: 20609 Sorted by model distance: nonbonded pdb=" OD1 ASP B 65 " pdb=" OH TYR B 107 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASN A 80 " pdb=" NE2 GLN B 7 " model vdw 2.397 3.120 nonbonded pdb=" OG SER A 18 " pdb=" OP1 G C 5 " model vdw 2.400 3.040 nonbonded pdb=" NE1 TRP B 32 " pdb=" OE2 GLU B 36 " model vdw 2.437 3.120 nonbonded pdb=" OE2 GLU A 5 " pdb=" OH TYR B 108 " model vdw 2.505 3.040 ... (remaining 20604 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 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.010 Set scattering table: 0.010 Process input model: 4.740 Find NCS groups from input model: 0.030 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 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 : 0.005 0.041 2729 Z= 0.331 Angle : 0.986 9.287 3852 Z= 0.804 Chirality : 0.058 0.177 450 Planarity : 0.007 0.050 372 Dihedral : 19.538 90.823 1256 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.00 % Allowed : 12.50 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.45), residues: 230 helix: -0.74 (0.34), residues: 166 sheet: None (None), residues: 0 loop : -1.68 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 73 TYR 0.026 0.003 TYR A 34 PHE 0.006 0.002 PHE B 78 TRP 0.020 0.003 TRP B 35 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.33 ( 2729) covalent geometry : angle 0.98564 / 0.80 ( 3852) hydrogen bonds : bond 0.16728 / 10.67 ( 147) hydrogen bonds : angle 5.55636 / 4.03 ( 406) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.092 Fit side-chains REVERT: A 4 LYS cc_start: 0.6660 (mttm) cc_final: 0.6442 (mttt) REVERT: A 49 GLU cc_start: 0.6105 (tp30) cc_final: 0.5531 (mt-10) REVERT: A 73 ARG cc_start: 0.4959 (ttt-90) cc_final: 0.4706 (ttt90) REVERT: B 30 ARG cc_start: 0.6693 (ttm170) cc_final: 0.6454 (ttp-170) REVERT: B 49 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5922 (mm-30) REVERT: B 61 MET cc_start: 0.4441 (mtm) cc_final: 0.4211 (mtm) REVERT: B 75 LYS cc_start: 0.6137 (mtpp) cc_final: 0.5726 (mtmm) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.8195 time to fit residues: 40.7891 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.218086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.182850 restraints weight = 2446.800| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 0.92 r_work: 0.3714 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2729 Z= 0.142 Angle : 0.514 4.642 3852 Z= 0.301 Chirality : 0.038 0.214 450 Planarity : 0.005 0.042 372 Dihedral : 19.290 90.517 794 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.00 % Allowed : 15.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.52), residues: 230 helix: 0.39 (0.37), residues: 174 sheet: None (None), residues: 0 loop : -1.66 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.014 0.002 TYR A 34 PHE 0.005 0.002 PHE A 78 TRP 0.010 0.002 TRP B 97 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 2729) covalent geometry : angle 0.51360 / 0.30 ( 3852) hydrogen bonds : bond 0.07538 / 4.92 ( 147) hydrogen bonds : angle 4.29348 / 3.08 ( 406) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.083 Fit side-chains REVERT: B 75 LYS cc_start: 0.7235 (mtpp) cc_final: 0.7004 (mtmm) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.8150 time to fit residues: 38.0852 Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.216210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.181353 restraints weight = 2444.515| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 0.92 r_work: 0.3679 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2729 Z= 0.141 Angle : 0.488 4.353 3852 Z= 0.283 Chirality : 0.036 0.124 450 Planarity : 0.005 0.050 372 Dihedral : 19.177 91.915 794 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.00 % Allowed : 14.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.55), residues: 230 helix: 0.86 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.67 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.010 0.002 TYR A 34 PHE 0.006 0.002 PHE A 78 TRP 0.009 0.002 TRP B 97 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 2729) covalent geometry : angle 0.48759 / 0.28 ( 3852) hydrogen bonds : bond 0.07021 / 4.58 ( 147) hydrogen bonds : angle 4.03510 / 2.89 ( 406) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.076 Fit side-chains REVERT: B 67 ARG cc_start: 0.6086 (mtm110) cc_final: 0.5514 (ttm110) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.6580 time to fit residues: 32.8387 Evaluate side-chains 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.213731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.183276 restraints weight = 2411.947| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 0.71 r_work: 0.3716 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2729 Z= 0.154 Angle : 0.503 3.555 3852 Z= 0.290 Chirality : 0.037 0.125 450 Planarity : 0.005 0.053 372 Dihedral : 19.183 92.226 794 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.50 % Allowed : 14.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.55), residues: 230 helix: 0.87 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.55 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 73 TYR 0.011 0.002 TYR A 107 PHE 0.009 0.003 PHE A 78 TRP 0.011 0.002 TRP B 97 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 2729) covalent geometry : angle 0.50343 / 0.29 ( 3852) hydrogen bonds : bond 0.07377 / 4.85 ( 147) hydrogen bonds : angle 4.06560 / 2.90 ( 406) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.077 Fit side-chains REVERT: B 61 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.4872 (ttm) REVERT: B 67 ARG cc_start: 0.6135 (mtm110) cc_final: 0.5691 (ttm110) outliers start: 11 outliers final: 7 residues processed: 47 average time/residue: 0.5549 time to fit residues: 26.5755 Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.215489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.183938 restraints weight = 2414.869| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 0.72 r_work: 0.3713 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2729 Z= 0.124 Angle : 0.436 2.892 3852 Z= 0.255 Chirality : 0.034 0.123 450 Planarity : 0.005 0.050 372 Dihedral : 19.058 91.877 794 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.00 % Allowed : 16.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.56), residues: 230 helix: 1.13 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.40 (0.86), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.009 0.002 TYR A 108 PHE 0.006 0.002 PHE A 78 TRP 0.006 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 2729) covalent geometry : angle 0.43628 / 0.26 ( 3852) hydrogen bonds : bond 0.06175 / 4.05 ( 147) hydrogen bonds : angle 3.87455 / 2.77 ( 406) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.051 Fit side-chains REVERT: B 61 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5000 (ttm) REVERT: B 67 ARG cc_start: 0.6187 (mtm110) cc_final: 0.5710 (ttm110) outliers start: 10 outliers final: 5 residues processed: 46 average time/residue: 0.6616 time to fit residues: 30.9204 Evaluate side-chains 47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.218589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.187720 restraints weight = 2433.659| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.76 r_work: 0.3769 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2729 Z= 0.100 Angle : 0.387 3.185 3852 Z= 0.227 Chirality : 0.031 0.122 450 Planarity : 0.004 0.046 372 Dihedral : 19.001 91.215 794 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.00 % Allowed : 17.00 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.57), residues: 230 helix: 1.39 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.38 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.003 0.001 PHE A 78 TRP 0.006 0.001 TRP A 35 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.10 ( 2729) covalent geometry : angle 0.38739 / 0.23 ( 3852) hydrogen bonds : bond 0.04939 / 3.22 ( 147) hydrogen bonds : angle 3.66332 / 2.61 ( 406) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.048 Fit side-chains REVERT: A 22 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 77 ARG cc_start: 0.7686 (mmt180) cc_final: 0.6961 (mmm-85) REVERT: B 67 ARG cc_start: 0.6135 (mtm110) cc_final: 0.5720 (ttm110) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.5877 time to fit residues: 26.2808 Evaluate side-chains 46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.215706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.182619 restraints weight = 2414.364| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 0.81 r_work: 0.3661 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2729 Z= 0.131 Angle : 0.437 3.127 3852 Z= 0.253 Chirality : 0.034 0.123 450 Planarity : 0.005 0.047 372 Dihedral : 19.055 91.242 794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.00 % Allowed : 15.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.56), residues: 230 helix: 1.29 (0.39), residues: 174 sheet: None (None), residues: 0 loop : -1.38 (0.85), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.011 0.002 TYR A 107 PHE 0.007 0.002 PHE A 78 TRP 0.008 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 2729) covalent geometry : angle 0.43698 / 0.25 ( 3852) hydrogen bonds : bond 0.05980 / 3.92 ( 147) hydrogen bonds : angle 3.78549 / 2.71 ( 406) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.049 Fit side-chains REVERT: A 22 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: B 61 MET cc_start: 0.5673 (OUTLIER) cc_final: 0.5455 (mtm) REVERT: B 67 ARG cc_start: 0.6100 (mtm110) cc_final: 0.5688 (ttm110) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.5890 time to fit residues: 26.9781 Evaluate side-chains 49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.0470 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.0770 chunk 12 optimal weight: 0.0070 chunk 22 optimal weight: 10.0000 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.220719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.192695 restraints weight = 2497.878| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 0.77 r_work: 0.3762 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2729 Z= 0.091 Angle : 0.374 3.487 3852 Z= 0.217 Chirality : 0.030 0.122 450 Planarity : 0.004 0.041 372 Dihedral : 18.989 90.260 794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.00 % Allowed : 17.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.56), residues: 230 helix: 1.44 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.37 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.008 0.001 TYR A 108 PHE 0.002 0.001 PHE A 78 TRP 0.008 0.001 TRP A 35 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.09 ( 2729) covalent geometry : angle 0.37392 / 0.22 ( 3852) hydrogen bonds : bond 0.04246 / 2.75 ( 147) hydrogen bonds : angle 3.57516 / 2.54 ( 406) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.081 Fit side-chains REVERT: A 22 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: A 77 ARG cc_start: 0.7482 (mmt180) cc_final: 0.6894 (mmm-85) REVERT: B 67 ARG cc_start: 0.6083 (mtm110) cc_final: 0.5749 (ttm110) REVERT: B 75 LYS cc_start: 0.7198 (mtpp) cc_final: 0.6951 (mtmm) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.8120 time to fit residues: 33.8502 Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.217892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.185342 restraints weight = 2474.640| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.78 r_work: 0.3781 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2729 Z= 0.110 Angle : 0.407 3.734 3852 Z= 0.235 Chirality : 0.032 0.122 450 Planarity : 0.004 0.041 372 Dihedral : 19.068 90.406 794 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.50 % Allowed : 18.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.56), residues: 230 helix: 1.42 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.38 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.009 0.002 TYR A 107 PHE 0.005 0.001 PHE A 78 TRP 0.006 0.001 TRP B 32 HIS 0.001 0.000 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 2729) covalent geometry : angle 0.40664 / 0.24 ( 3852) hydrogen bonds : bond 0.05107 / 3.34 ( 147) hydrogen bonds : angle 3.65998 / 2.62 ( 406) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.083 Fit side-chains REVERT: A 22 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: A 77 ARG cc_start: 0.7654 (mmt180) cc_final: 0.6974 (mmm-85) REVERT: B 67 ARG cc_start: 0.5993 (mtm110) cc_final: 0.5544 (ttm110) REVERT: B 75 LYS cc_start: 0.7228 (mtpp) cc_final: 0.6928 (mtmm) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.7729 time to fit residues: 32.2439 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.219705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.186714 restraints weight = 2514.089| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 0.80 r_work: 0.3767 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2729 Z= 0.095 Angle : 0.390 4.087 3852 Z= 0.223 Chirality : 0.031 0.120 450 Planarity : 0.004 0.037 372 Dihedral : 19.053 89.802 794 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.50 % Allowed : 18.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.56), residues: 230 helix: 1.46 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.32 (0.83), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.009 0.001 TYR A 108 PHE 0.002 0.001 PHE A 78 TRP 0.005 0.001 TRP A 35 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.10 ( 2729) covalent geometry : angle 0.38965 / 0.22 ( 3852) hydrogen bonds : bond 0.04450 / 2.90 ( 147) hydrogen bonds : angle 3.60812 / 2.59 ( 406) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.085 Fit side-chains REVERT: A 22 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: A 77 ARG cc_start: 0.7518 (mmt180) cc_final: 0.6922 (mmm-85) REVERT: B 67 ARG cc_start: 0.6114 (mtm110) cc_final: 0.5800 (ttm110) REVERT: B 75 LYS cc_start: 0.7158 (mtpp) cc_final: 0.6911 (mtmm) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.8069 time to fit residues: 32.8505 Evaluate side-chains 41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 40 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 overall best weight: 1.6624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.216670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.185429 restraints weight = 2475.190| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 0.70 r_work: 0.3747 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2729 Z= 0.130 Angle : 0.453 4.556 3852 Z= 0.258 Chirality : 0.033 0.124 450 Planarity : 0.004 0.037 372 Dihedral : 19.161 90.288 794 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.00 % Allowed : 18.50 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.56), residues: 230 helix: 1.34 (0.40), residues: 174 sheet: None (None), residues: 0 loop : -1.31 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.011 0.002 TYR A 107 PHE 0.007 0.002 PHE A 78 TRP 0.008 0.002 TRP B 97 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 2729) covalent geometry : angle 0.45256 / 0.26 ( 3852) hydrogen bonds : bond 0.05818 / 3.82 ( 147) hydrogen bonds : angle 3.78460 / 2.72 ( 406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1160.57 seconds wall clock time: 20 minutes 27.29 seconds (1227.29 seconds total)