Starting phenix.real_space_refine on Sat Oct 24 03:54:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.cif Found real_map, /net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.map" model { file = "/net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36uk_77868/10_2026/36uk_77868.cif" } resolution = 2.8 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= 0.006 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 515 5.49 5 Mg 24 5.21 5 S 3 5.16 5 C 5530 2.51 5 N 2190 2.21 5 O 3748 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 13, 'rna3p_pur': 218, 'rna3p_pyr': 161} Link IDs: {'rna2p': 38, 'rna3p': 378} 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: "C" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1889 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 34, 'rna3p_pyr': 41} Link IDs: {'rna2p': 14, 'rna3p': 74} Chain: "E" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Unusual residues: {' MG': 24} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 12010 At special positions: 0 Unit cell: (130.003, 139.373, 173.338, 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 515 15.00 Mg 24 11.99 O 3748 8.00 N 2190 7.00 C 5530 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: 0.88 Conformation dependent library (CDL) restraints added in 189.4 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: 6 helices and 1 sheets defined 52.6% alpha, 16.4% beta 175 base pairs and 281 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.521A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 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 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.504A pdb=" N THR B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 447 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 175 basepair parallelities 281 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.27 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: 1300 1.33 - 1.45: 6535 1.45 - 1.57: 4447 1.57 - 1.69: 1028 1.69 - 1.81: 5 Bond restraints: 13315 Sorted by residual: bond pdb=" N9 A A 350 " pdb=" C4 A A 350 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 5.01e+00 bond pdb=" N9 A A 266 " pdb=" C4 A A 266 " ideal model delta sigma weight residual 1.374 1.386 -0.012 6.00e-03 2.78e+04 3.92e+00 bond pdb=" CB GLU B 91 " pdb=" CG GLU B 91 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" N7 A A 385 " pdb=" C5 A A 385 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.82e+00 bond pdb=" N9 A A 100 " pdb=" C4 A A 100 " ideal model delta sigma weight residual 1.374 1.364 0.010 6.00e-03 2.78e+04 2.57e+00 ... (remaining 13310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 18873 1.81 - 3.63: 1620 3.63 - 5.44: 44 5.44 - 7.26: 6 7.26 - 9.07: 3 Bond angle restraints: 20546 Sorted by residual: angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C6 C A 318 " ideal model delta sigma weight residual 120.80 127.26 -6.46 1.20e+00 6.94e-01 2.90e+01 angle pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sigma weight residual 118.80 112.93 5.87 1.10e+00 8.26e-01 2.85e+01 angle pdb=" N1 C A 318 " pdb=" C2 C A 318 " pdb=" O2 C A 318 " ideal model delta sigma weight residual 118.90 115.76 3.14 6.00e-01 2.78e+00 2.74e+01 angle pdb=" C3' U C 46 " pdb=" O3' U C 46 " pdb=" P C C 47 " ideal model delta sigma weight residual 119.70 125.76 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" O5' C A 235 " pdb=" C5' C A 235 " pdb=" C4' C A 235 " ideal model delta sigma weight residual 109.40 113.38 -3.98 8.00e-01 1.56e+00 2.47e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 7258 35.98 - 71.95: 1256 71.95 - 107.93: 151 107.93 - 143.91: 2 143.91 - 179.89: 9 Dihedral angle restraints: 8676 sinusoidal: 8339 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 9.30 -169.30 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U C 59 " pdb=" C1' U C 59 " pdb=" N1 U C 59 " pdb=" C2 U C 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.11 179.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 235 " pdb=" C1' C A 235 " pdb=" N1 C A 235 " pdb=" C2 C A 235 " ideal model delta sinusoidal sigma weight residual -128.00 50.96 -178.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1860 0.041 - 0.083: 277 0.083 - 0.124: 117 0.124 - 0.166: 448 0.166 - 0.207: 9 Chirality restraints: 2711 Sorted by residual: chirality pdb=" C3' U A 407 " pdb=" C4' U A 407 " pdb=" O3' U A 407 " pdb=" C2' U A 407 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' U C 46 " pdb=" C4' U C 46 " pdb=" O3' U C 46 " pdb=" C2' U C 46 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" C1' G A 328 " pdb=" O4' G A 328 " pdb=" C2' G A 328 " pdb=" N9 G A 328 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 2708 not shown) Planarity restraints: 679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 298 " 0.037 2.00e-02 2.50e+03 1.53e-02 6.98e+00 pdb=" N9 G A 298 " -0.035 2.00e-02 2.50e+03 pdb=" C8 G A 298 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 298 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 298 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 298 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 298 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A 298 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 298 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 298 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A 298 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A 298 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " -0.030 2.00e-02 2.50e+03 1.42e-02 4.51e+00 pdb=" N1 C A 318 " 0.025 2.00e-02 2.50e+03 pdb=" C2 C A 318 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 318 " 0.006 2.00e-02 2.50e+03 pdb=" N3 C A 318 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 318 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 318 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C A 318 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 318 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 356 " -0.028 2.00e-02 2.50e+03 1.20e-02 3.94e+00 pdb=" N9 A A 356 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 356 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 356 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 356 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A A 356 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A 356 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 356 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A 356 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A 356 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A 356 " 0.007 2.00e-02 2.50e+03 ... (remaining 676 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 66 2.58 - 3.16: 8804 3.16 - 3.74: 26590 3.74 - 4.32: 35286 4.32 - 4.90: 42356 Nonbonded interactions: 113102 Sorted by model distance: nonbonded pdb=" OP1 C C 73 " pdb="MG MG A 512 " model vdw 1.994 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 515 " model vdw 1.996 2.170 nonbonded pdb=" OP2 G C 1 " pdb="MG MG A 506 " model vdw 2.001 2.170 nonbonded pdb=" OP2 C A 103 " pdb="MG MG A 513 " model vdw 2.001 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 512 " model vdw 2.020 2.170 ... (remaining 113097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.003 0.056 13315 Z= 0.298 Angle : 0.844 9.072 20546 Z= 0.711 Chirality : 0.064 0.207 2711 Planarity : 0.004 0.025 679 Dihedral : 25.678 179.886 8460 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.04 % Allowed : 35.35 % 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: 1.46 (0.84), residues: 114 helix: 2.28 (0.81), residues: 46 sheet: 1.33 (1.09), residues: 28 loop : -0.92 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.010 0.001 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.30 (13315) covalent geometry : angle 0.84414 / 0.71 (20546) hydrogen bonds : bond 0.07494 / 7.32 ( 495) hydrogen bonds : angle 2.40046 / 2.95 ( 882) *********************** 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 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.136 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.8653 time to fit residues: 16.5602 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [54, 24, 48, 56, 26, 2, 16, 32, 31, 25, 58] chunk 54 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 40.0000 overall best weight: 6.9592 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066404 restraints weight = 33576.559| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.26 r_work: 0.2850 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 13315 Z= 0.554 Angle : 0.978 13.040 20546 Z= 0.484 Chirality : 0.068 0.370 2711 Planarity : 0.009 0.047 679 Dihedral : 25.834 179.070 8212 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 9.09 % Allowed : 23.23 % Favored : 67.68 % 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: 0.74 (0.78), residues: 114 helix: 1.38 (0.71), residues: 47 sheet: 1.38 (1.02), residues: 26 loop : -1.18 (0.98), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 65 TYR 0.013 0.003 TYR B 94 PHE 0.022 0.005 PHE B 68 HIS 0.002 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.55 (13315) covalent geometry : angle 0.97773 / 0.48 (20546) hydrogen bonds : bond 0.14082 / 15.33 ( 495) hydrogen bonds : angle 2.70788 / 3.40 ( 882) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.167 Fit side-chains REVERT: B 71 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9129 (pp) outliers start: 9 outliers final: 4 residues processed: 20 average time/residue: 0.7516 time to fit residues: 16.1574 Evaluate side-chains 18 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [23, 45, 22, 56, 27, 1, 44, 4, 53, 36, 37] chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 36 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.116466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067772 restraints weight = 33825.833| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 0.79 r_work: 0.2878 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13315 Z= 0.346 Angle : 0.693 8.450 20546 Z= 0.372 Chirality : 0.048 0.381 2711 Planarity : 0.007 0.039 679 Dihedral : 25.928 179.132 8207 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % Favored : 66.67 % 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: 1.22 (0.80), residues: 114 helix: 2.14 (0.75), residues: 47 sheet: 1.53 (1.04), residues: 26 loop : -1.34 (0.94), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.014 0.002 TYR B 94 PHE 0.014 0.003 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.35 (13315) covalent geometry : angle 0.69324 / 0.37 (20546) hydrogen bonds : bond 0.09804 / 10.51 ( 495) hydrogen bonds : angle 2.38289 / 2.97 ( 882) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 14 time to evaluate : 0.138 Fit side-chains REVERT: B 18 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: B 71 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9113 (pp) outliers start: 9 outliers final: 5 residues processed: 20 average time/residue: 0.7513 time to fit residues: 16.0663 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [59, 18, 32, 44, 15, 28, 46, 26, 0, 52, 54] chunk 59 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 52 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.113560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070805 restraints weight = 34549.664| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.64 r_work: 0.2884 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 13315 Z= 0.488 Angle : 0.899 9.907 20546 Z= 0.458 Chirality : 0.063 0.393 2711 Planarity : 0.008 0.041 679 Dihedral : 26.032 178.911 8207 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 11.11 % Allowed : 18.18 % 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: 0.93 (0.80), residues: 114 helix: 1.72 (0.73), residues: 47 sheet: 1.29 (1.10), residues: 26 loop : -1.18 (0.96), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.017 0.003 TYR B 94 PHE 0.014 0.004 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.49 (13315) covalent geometry : angle 0.89902 / 0.46 (20546) hydrogen bonds : bond 0.13893 / 15.03 ( 495) hydrogen bonds : angle 2.63757 / 3.33 ( 882) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 13 time to evaluate : 0.149 Fit side-chains REVERT: B 18 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: B 71 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9073 (pp) outliers start: 11 outliers final: 5 residues processed: 20 average time/residue: 0.7761 time to fit residues: 16.6222 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 12 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU 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: 60 random chunks: [38, 5, 55, 23, 30, 42, 57, 48, 27, 20, 58] chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 50.0000 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.115241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.070309 restraints weight = 33967.343| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.10 r_work: 0.2898 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13315 Z= 0.338 Angle : 0.690 8.044 20546 Z= 0.374 Chirality : 0.048 0.386 2711 Planarity : 0.007 0.040 679 Dihedral : 26.054 179.751 8207 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 8.08 % Allowed : 22.22 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.82), residues: 114 helix: 2.10 (0.75), residues: 47 sheet: 0.78 (1.08), residues: 28 loop : -0.97 (1.00), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.017 0.002 TYR B 94 PHE 0.012 0.003 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.34 (13315) covalent geometry : angle 0.68984 / 0.37 (20546) hydrogen bonds : bond 0.10172 / 10.95 ( 495) hydrogen bonds : angle 2.37708 / 3.02 ( 882) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.159 Fit side-chains REVERT: B 18 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: B 71 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9082 (pp) outliers start: 8 outliers final: 5 residues processed: 20 average time/residue: 0.6689 time to fit residues: 14.4238 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [33, 50, 28, 12, 27, 9, 6, 2, 21, 38, 22] chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 50.0000 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.114741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070739 restraints weight = 33921.887| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.44 r_work: 0.2909 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13315 Z= 0.405 Angle : 0.785 9.027 20546 Z= 0.410 Chirality : 0.055 0.390 2711 Planarity : 0.007 0.043 679 Dihedral : 26.042 179.528 8207 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 10.10 % Allowed : 20.20 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.81), residues: 114 helix: 1.95 (0.74), residues: 47 sheet: 0.73 (1.08), residues: 28 loop : -0.90 (1.01), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.013 0.002 TYR B 94 PHE 0.012 0.003 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.40 (13315) covalent geometry : angle 0.78530 / 0.41 (20546) hydrogen bonds : bond 0.11898 / 12.81 ( 495) hydrogen bonds : angle 2.49250 / 3.17 ( 882) *********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 13 time to evaluate : 0.152 Fit side-chains REVERT: B 18 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: B 71 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9114 (pp) outliers start: 10 outliers final: 5 residues processed: 19 average time/residue: 0.7409 time to fit residues: 15.1297 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 12 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [36, 25, 16, 39, 13, 43, 7, 33, 23, 37, 29] chunk 36 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.117174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074733 restraints weight = 33832.046| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.02 r_work: 0.2951 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13315 Z= 0.354 Angle : 0.694 8.671 20546 Z= 0.374 Chirality : 0.049 0.387 2711 Planarity : 0.007 0.042 679 Dihedral : 26.063 179.995 8207 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % Favored : 66.67 % 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: 1.16 (0.82), residues: 114 helix: 2.08 (0.74), residues: 47 sheet: 0.79 (1.08), residues: 28 loop : -0.90 (1.02), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.013 0.002 TYR B 94 PHE 0.013 0.003 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.35 (13315) covalent geometry : angle 0.69431 / 0.37 (20546) hydrogen bonds : bond 0.10085 / 10.82 ( 495) hydrogen bonds : angle 2.39167 / 3.04 ( 882) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.161 Fit side-chains REVERT: B 18 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: B 71 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9060 (pp) outliers start: 9 outliers final: 5 residues processed: 22 average time/residue: 0.8323 time to fit residues: 19.5028 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [56, 59, 27, 12, 4, 39, 6, 2, 26, 37, 50] chunk 56 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 50 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.114535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071053 restraints weight = 33806.682| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.34 r_work: 0.2916 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13315 Z= 0.434 Angle : 0.821 9.525 20546 Z= 0.423 Chirality : 0.057 0.391 2711 Planarity : 0.008 0.045 679 Dihedral : 26.052 179.663 8207 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 9.09 % Allowed : 25.25 % Favored : 65.66 % 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: 0.89 (0.81), residues: 114 helix: 1.94 (0.73), residues: 47 sheet: 0.55 (1.06), residues: 28 loop : -1.04 (1.03), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 65 TYR 0.014 0.002 TYR B 94 PHE 0.017 0.004 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.43 (13315) covalent geometry : angle 0.82093 / 0.42 (20546) hydrogen bonds : bond 0.11943 / 12.84 ( 495) hydrogen bonds : angle 2.50916 / 3.17 ( 882) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 13 time to evaluate : 0.158 Fit side-chains REVERT: B 18 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8565 (mt0) REVERT: B 71 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9098 (pp) outliers start: 9 outliers final: 5 residues processed: 19 average time/residue: 0.7804 time to fit residues: 15.8616 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 13 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [16, 22, 7, 51, 11, 9, 59, 2, 33, 29, 28] chunk 16 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.074431 restraints weight = 33569.413| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.68 r_work: 0.2991 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13315 Z= 0.312 Angle : 0.668 8.023 20546 Z= 0.364 Chirality : 0.046 0.386 2711 Planarity : 0.007 0.042 679 Dihedral : 26.045 179.747 8207 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 8.08 % Allowed : 26.26 % Favored : 65.66 % 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: 1.06 (0.82), residues: 114 helix: 2.18 (0.75), residues: 47 sheet: 0.46 (1.04), residues: 28 loop : -0.95 (1.04), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.016 0.002 TYR B 94 PHE 0.016 0.003 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.31 (13315) covalent geometry : angle 0.66790 / 0.36 (20546) hydrogen bonds : bond 0.09735 / 10.44 ( 495) hydrogen bonds : angle 2.38094 / 3.02 ( 882) *********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 14 time to evaluate : 0.256 Fit side-chains REVERT: B 18 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: B 71 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9056 (pp) outliers start: 8 outliers final: 5 residues processed: 20 average time/residue: 0.7278 time to fit residues: 15.6924 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [41, 22, 45, 4, 29, 58, 43, 26, 8, 33, 13] chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074881 restraints weight = 33853.944| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.55 r_work: 0.3017 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13315 Z= 0.253 Angle : 0.609 9.553 20546 Z= 0.340 Chirality : 0.042 0.383 2711 Planarity : 0.006 0.041 679 Dihedral : 25.947 179.670 8207 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % 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: 1.11 (0.82), residues: 114 helix: 2.29 (0.76), residues: 47 sheet: 0.30 (1.01), residues: 28 loop : -0.86 (1.07), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.015 0.002 TYR B 94 PHE 0.012 0.003 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.25 (13315) covalent geometry : angle 0.60856 / 0.34 (20546) hydrogen bonds : bond 0.08944 / 9.61 ( 495) hydrogen bonds : angle 2.31774 / 2.95 ( 882) ********************** 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 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 15 time to evaluate : 0.158 Fit side-chains REVERT: B 71 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9023 (pp) outliers start: 7 outliers final: 5 residues processed: 20 average time/residue: 0.6811 time to fit residues: 14.7163 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: [53, 30, 22, 0, 6, 11, 33, 34, 52, 24, 4] chunk 53 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.120152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.082459 restraints weight = 37026.962| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.45 r_work: 0.3109 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.075 13315 Z= 0.617 Angle : 1.043 12.168 20546 Z= 0.509 Chirality : 0.072 0.399 2711 Planarity : 0.009 0.048 679 Dihedral : 26.100 179.723 8207 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 27.27 % Favored : 65.66 % 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: 0.23 (0.78), residues: 114 helix: 1.37 (0.74), residues: 47 sheet: -0.03 (0.98), residues: 28 loop : -1.14 (1.01), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 65 TYR 0.012 0.002 TYR B 94 PHE 0.023 0.005 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.62 (13315) covalent geometry : angle 1.04279 / 0.51 (20546) hydrogen bonds : bond 0.14518 / 15.66 ( 495) hydrogen bonds : angle 2.75475 / 3.44 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5536.86 seconds wall clock time: 94 minutes 46.53 seconds (5686.53 seconds total)