Starting phenix.real_space_refine on Thu Jul 2 19:50:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.map" model { file = "/net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zi8_74265/07_2026/9zi8_74265.cif" } resolution = 3.18 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 34 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9943 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 16, 'rna3p_pur': 220, 'rna3p_pyr': 158} Link IDs: {'rna2p': 39, 'rna3p': 377} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Unusual residues: {' MG': 34} Classifications: {'undetermined': 34} Link IDs: {None: 33} Time building chain proxies: 1.58, per 1000 atoms: 0.16 Number of scatterers: 9943 At special positions: 0 Unit cell: (125.172, 171.288, 142.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 34 11.99 O 3051 8.00 N 1834 7.00 C 4604 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: 0.68 Conformation dependent library (CDL) restraints added in 63.7 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 46.6% alpha, 18.1% beta 139 base pairs and 217 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 49 through 52 removed outlier: 4.032A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.585A pdb=" N PHE B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 42 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 85 " --> pdb=" O SER B 46 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 217 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1101 1.33 - 1.45: 5386 1.45 - 1.57: 3675 1.57 - 1.69: 833 1.69 - 1.81: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N1 U A 264 " pdb=" C2 U A 264 " ideal model delta sigma weight residual 1.381 1.402 -0.021 9.00e-03 1.23e+04 5.61e+00 bond pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sigma weight residual 1.397 1.377 0.020 1.00e-02 1.00e+04 4.11e+00 bond pdb=" N9 G A 372 " pdb=" C4 G A 372 " ideal model delta sigma weight residual 1.375 1.390 -0.015 8.00e-03 1.56e+04 3.51e+00 bond pdb=" N9 A A 374 " pdb=" C4 A A 374 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.86e+00 bond pdb=" N9 A A 189 " pdb=" C4 A A 189 " ideal model delta sigma weight residual 1.374 1.384 -0.010 6.00e-03 2.78e+04 2.59e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16753 2.25 - 4.49: 162 4.49 - 6.74: 25 6.74 - 8.98: 3 8.98 - 11.23: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" N1 C A 318 " pdb=" C2 C A 318 " pdb=" O2 C A 318 " ideal model delta sigma weight residual 118.90 114.88 4.02 6.00e-01 2.78e+00 4.50e+01 angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sigma weight residual 118.80 111.56 7.24 1.10e+00 8.26e-01 4.33e+01 angle pdb=" N1 U A 264 " pdb=" C2 U A 264 " pdb=" O2 U A 264 " ideal model delta sigma weight residual 122.80 127.32 -4.52 7.00e-01 2.04e+00 4.17e+01 angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C6 C A 318 " ideal model delta sigma weight residual 120.80 128.40 -7.60 1.20e+00 6.94e-01 4.01e+01 angle pdb=" O2 U A 264 " pdb=" C2 U A 264 " pdb=" N3 U A 264 " ideal model delta sigma weight residual 122.20 117.77 4.43 7.00e-01 2.04e+00 4.00e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 5906 33.05 - 66.09: 1049 66.09 - 99.14: 150 99.14 - 132.19: 5 132.19 - 165.23: 6 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual 200.00 39.85 160.15 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U A 267 " pdb=" C1' U A 267 " pdb=" N1 U A 267 " pdb=" C2 U A 267 " ideal model delta sinusoidal sigma weight residual 200.00 44.54 155.46 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U A 264 " pdb=" C1' U A 264 " pdb=" N1 U A 264 " pdb=" C2 U A 264 " ideal model delta sinusoidal sigma weight residual 232.00 148.36 83.64 1 1.70e+01 3.46e-03 2.95e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2043 0.047 - 0.094: 130 0.094 - 0.140: 37 0.140 - 0.187: 7 0.187 - 0.234: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P U A 33 " pdb=" OP1 U A 33 " pdb=" OP2 U A 33 " pdb=" O5' U A 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' U A 171 " pdb=" C4' U A 171 " pdb=" O3' U A 171 " pdb=" C2' U A 171 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C1' G A 234 " pdb=" O4' G A 234 " pdb=" C2' G A 234 " pdb=" N9 G A 234 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " -0.038 2.00e-02 2.50e+03 1.66e-02 8.29e+00 pdb=" N9 G A 32 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G A 32 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 32 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 32 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G A 32 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 32 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 32 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 32 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 32 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 231 " 0.035 2.00e-02 2.50e+03 1.53e-02 6.48e+00 pdb=" N9 A A 231 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A A 231 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A A 231 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A A 231 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 231 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A 231 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A A 231 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A 231 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 231 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A 231 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.032 2.00e-02 2.50e+03 1.40e-02 5.90e+00 pdb=" N9 G A 298 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.003 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 35 2.53 - 3.12: 6881 3.12 - 3.71: 20974 3.71 - 4.31: 27810 4.31 - 4.90: 34942 Nonbonded interactions: 90642 Sorted by model distance: nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 509 " model vdw 1.935 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 512 " model vdw 1.981 2.170 nonbonded pdb=" OP2 A A 390 " pdb="MG MG A 505 " model vdw 1.987 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 509 " model vdw 2.014 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 513 " model vdw 2.025 2.170 ... (remaining 90637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.120 Find NCS groups from input model: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 : 0.002 0.042 11000 Z= 0.224 Angle : 0.594 11.231 16944 Z= 0.545 Chirality : 0.030 0.234 2221 Planarity : 0.004 0.030 581 Dihedral : 25.508 165.232 6900 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 29.29 % Favored : 70.71 % 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: 0.64 (0.82), residues: 114 helix: 2.46 (0.83), residues: 44 sheet: 0.76 (0.98), residues: 28 loop : -2.20 (0.87), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 59 TYR 0.023 0.002 TYR B 5 PHE 0.008 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.22 (11000) covalent geometry : angle 0.59421 / 0.55 (16944) hydrogen bonds : bond 0.08866 / 8.14 ( 404) hydrogen bonds : angle 3.31715 / 3.83 ( 752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.101 Fit side-chains REVERT: B 12 GLU cc_start: 0.9018 (mp0) cc_final: 0.8749 (mp0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0568 time to fit residues: 2.3789 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.090358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051505 restraints weight = 56198.866| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.15 r_work: 0.2740 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 11000 Z= 0.521 Angle : 0.757 10.327 16944 Z= 0.445 Chirality : 0.052 0.274 2221 Planarity : 0.007 0.036 581 Dihedral : 25.763 165.374 6645 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Rotamer: Outliers : 4.04 % Allowed : 32.32 % Favored : 63.64 % 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: -0.38 (0.75), residues: 114 helix: 1.11 (0.76), residues: 44 sheet: 0.29 (0.90), residues: 28 loop : -2.16 (0.89), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 57 TYR 0.017 0.003 TYR B 81 PHE 0.035 0.005 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.52 (11000) covalent geometry : angle 0.75735 / 0.45 (16944) hydrogen bonds : bond 0.12276 / 11.17 ( 404) hydrogen bonds : angle 3.11882 / 3.62 ( 752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.095 Fit side-chains REVERT: B 12 GLU cc_start: 0.9282 (mp0) cc_final: 0.8930 (mp0) outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 0.0617 time to fit residues: 2.3730 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.090773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051551 restraints weight = 56002.979| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.51 r_work: 0.2753 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11000 Z= 0.307 Angle : 0.585 10.120 16944 Z= 0.359 Chirality : 0.040 0.252 2221 Planarity : 0.005 0.028 581 Dihedral : 25.872 165.638 6645 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.02 % Favored : 92.11 % Rotamer: Outliers : 2.02 % Allowed : 37.37 % Favored : 60.61 % 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: -0.05 (0.79), residues: 114 helix: 1.97 (0.82), residues: 44 sheet: -0.58 (0.82), residues: 31 loop : -1.93 (0.96), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.015 0.002 TYR B 31 PHE 0.021 0.004 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.31 (11000) covalent geometry : angle 0.58545 / 0.36 (16944) hydrogen bonds : bond 0.09393 / 8.19 ( 404) hydrogen bonds : angle 2.74487 / 3.23 ( 752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.102 Fit side-chains REVERT: B 12 GLU cc_start: 0.9279 (mp0) cc_final: 0.8962 (mp0) outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.0573 time to fit residues: 2.4483 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.089634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051773 restraints weight = 52939.741| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.15 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11000 Z= 0.333 Angle : 0.623 10.735 16944 Z= 0.379 Chirality : 0.042 0.262 2221 Planarity : 0.005 0.028 581 Dihedral : 25.931 164.735 6645 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 5.05 % Allowed : 35.35 % Favored : 59.60 % 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: 0.07 (0.79), residues: 114 helix: 1.80 (0.82), residues: 44 sheet: -0.13 (0.81), residues: 29 loop : -1.80 (0.99), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.014 0.002 TYR B 31 PHE 0.018 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.33 (11000) covalent geometry : angle 0.62299 / 0.38 (16944) hydrogen bonds : bond 0.10353 / 9.13 ( 404) hydrogen bonds : angle 2.72751 / 3.22 ( 752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.9059 (mp0) cc_final: 0.8762 (mp0) outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.0721 time to fit residues: 2.8880 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 50.0000 chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.088987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048890 restraints weight = 56380.572| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.65 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 11000 Z= 0.538 Angle : 0.808 10.165 16944 Z= 0.474 Chirality : 0.053 0.287 2221 Planarity : 0.006 0.030 581 Dihedral : 26.173 165.629 6645 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 27.88 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.60 % Rotamer: Outliers : 12.12 % Allowed : 32.32 % Favored : 55.56 % 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: -0.49 (0.82), residues: 114 helix: 1.16 (0.76), residues: 46 sheet: -1.06 (0.81), residues: 31 loop : -1.45 (1.24), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 6 TYR 0.018 0.003 TYR B 31 PHE 0.022 0.006 PHE B 13 HIS 0.008 0.005 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00893 / 0.54 (11000) covalent geometry : angle 0.80822 / 0.47 (16944) hydrogen bonds : bond 0.14007 / 12.61 ( 404) hydrogen bonds : angle 3.21413 / 3.93 ( 752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.089 Fit side-chains REVERT: B 12 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: B 23 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (m) REVERT: B 86 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7926 (mtm-85) REVERT: B 107 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8685 (mtpp) outliers start: 12 outliers final: 3 residues processed: 31 average time/residue: 0.0769 time to fit residues: 3.3872 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 TYR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.090716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.054007 restraints weight = 57056.384| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.47 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11000 Z= 0.197 Angle : 0.556 10.338 16944 Z= 0.346 Chirality : 0.038 0.248 2221 Planarity : 0.005 0.035 581 Dihedral : 26.065 164.954 6645 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.02 % Favored : 92.11 % Rotamer: Outliers : 6.06 % Allowed : 38.38 % Favored : 55.56 % 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: 0.78 (0.85), residues: 114 helix: 2.73 (0.84), residues: 43 sheet: -0.03 (0.82), residues: 29 loop : -1.50 (1.10), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.012 0.002 TYR B 31 PHE 0.013 0.003 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.20 (11000) covalent geometry : angle 0.55566 / 0.35 (16944) hydrogen bonds : bond 0.08468 / 7.23 ( 404) hydrogen bonds : angle 2.59085 / 3.02 ( 752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.170 Fit side-chains REVERT: B 3 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9099 (mtmm) REVERT: B 12 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8816 (mp0) REVERT: B 107 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8655 (mtpp) outliers start: 6 outliers final: 2 residues processed: 31 average time/residue: 0.0951 time to fit residues: 4.2853 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.088374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.049843 restraints weight = 56744.064| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.54 r_work: 0.2709 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.096 11000 Z= 0.677 Angle : 0.899 10.303 16944 Z= 0.522 Chirality : 0.059 0.309 2221 Planarity : 0.007 0.034 581 Dihedral : 26.206 164.730 6645 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 30.59 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 36.36 % Favored : 52.53 % 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: -0.90 (0.80), residues: 114 helix: 0.53 (0.72), residues: 47 sheet: -1.05 (0.80), residues: 31 loop : -1.50 (1.26), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 6 TYR 0.025 0.004 TYR B 31 PHE 0.028 0.007 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01126 / 0.68 (11000) covalent geometry : angle 0.89921 / 0.52 (16944) hydrogen bonds : bond 0.14802 / 13.47 ( 404) hydrogen bonds : angle 3.28939 / 4.03 ( 752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.172 Fit side-chains REVERT: B 9 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8362 (mtmm) REVERT: B 12 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9018 (mp0) REVERT: B 107 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8693 (mtpp) outliers start: 11 outliers final: 8 residues processed: 28 average time/residue: 0.1097 time to fit residues: 4.4383 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.089038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052115 restraints weight = 56455.820| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.85 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11000 Z= 0.442 Angle : 0.710 10.078 16944 Z= 0.425 Chirality : 0.049 0.276 2221 Planarity : 0.006 0.036 581 Dihedral : 26.191 164.776 6645 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 10.10 % Allowed : 39.39 % Favored : 50.51 % 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: -0.41 (0.82), residues: 114 helix: 1.44 (0.77), residues: 44 sheet: -0.97 (0.80), residues: 31 loop : -1.60 (1.20), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 106 TYR 0.015 0.003 TYR B 31 PHE 0.018 0.004 PHE B 13 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.44 (11000) covalent geometry : angle 0.70974 / 0.42 (16944) hydrogen bonds : bond 0.11643 / 10.22 ( 404) hydrogen bonds : angle 2.96224 / 3.57 ( 752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.149 Fit side-chains REVERT: B 12 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8893 (mp0) REVERT: B 87 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8993 (tm-30) REVERT: B 107 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8641 (mtpp) outliers start: 10 outliers final: 7 residues processed: 30 average time/residue: 0.0906 time to fit residues: 4.0761 Evaluate side-chains 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.090291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053776 restraints weight = 56673.842| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.53 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11000 Z= 0.203 Angle : 0.560 9.946 16944 Z= 0.347 Chirality : 0.039 0.237 2221 Planarity : 0.005 0.035 581 Dihedral : 26.089 165.466 6645 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Rotamer: Outliers : 7.07 % Allowed : 40.40 % Favored : 52.53 % 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: 0.81 (0.87), residues: 114 helix: 2.59 (0.87), residues: 43 sheet: 0.01 (0.81), residues: 29 loop : -1.31 (1.15), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.010 0.002 TYR B 31 PHE 0.012 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.20 (11000) covalent geometry : angle 0.55960 / 0.35 (16944) hydrogen bonds : bond 0.08249 / 7.00 ( 404) hydrogen bonds : angle 2.68203 / 3.28 ( 752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.157 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 31 average time/residue: 0.0912 time to fit residues: 4.2536 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 50.0000 chunk 46 optimal weight: 0.0670 chunk 35 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 50.0000 overall best weight: 5.4126 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.088395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.053151 restraints weight = 51415.964| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.52 r_work: 0.2743 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 11000 Z= 0.424 Angle : 0.672 9.863 16944 Z= 0.403 Chirality : 0.047 0.268 2221 Planarity : 0.005 0.032 581 Dihedral : 26.078 164.727 6645 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.65 % Favored : 89.47 % Rotamer: Outliers : 6.06 % Allowed : 39.39 % Favored : 54.55 % 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: 0.16 (0.86), residues: 114 helix: 2.00 (0.83), residues: 43 sheet: -0.94 (0.78), residues: 31 loop : -1.05 (1.25), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.017 0.002 TYR B 31 PHE 0.021 0.004 PHE B 28 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.42 (11000) covalent geometry : angle 0.67164 / 0.40 (16944) hydrogen bonds : bond 0.10711 / 9.42 ( 404) hydrogen bonds : angle 2.90454 / 3.60 ( 752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.142 Fit side-chains REVERT: B 9 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8234 (mtmm) REVERT: B 11 GLU cc_start: 0.8817 (mp0) cc_final: 0.8574 (tm-30) REVERT: B 23 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8273 (m) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.0901 time to fit residues: 3.8164 Evaluate side-chains 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.090360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053860 restraints weight = 57390.373| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.53 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11000 Z= 0.181 Angle : 0.548 9.600 16944 Z= 0.340 Chirality : 0.038 0.230 2221 Planarity : 0.005 0.033 581 Dihedral : 26.036 167.079 6645 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Rotamer: Outliers : 6.06 % Allowed : 39.39 % Favored : 54.55 % 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: 1.13 (0.90), residues: 114 helix: 2.88 (0.90), residues: 43 sheet: 0.03 (0.83), residues: 29 loop : -1.03 (1.20), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 6 TYR 0.009 0.002 TYR B 31 PHE 0.013 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.18 (11000) covalent geometry : angle 0.54803 / 0.34 (16944) hydrogen bonds : bond 0.08078 / 6.89 ( 404) hydrogen bonds : angle 2.67377 / 3.29 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3317.90 seconds wall clock time: 57 minutes 29.18 seconds (3449.18 seconds total)