Starting phenix.real_space_refine on Wed Aug 5 13:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zid_74270/08_2026/9zid_74270.map" } resolution = 3.4 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 417 5.49 5 Mg 29 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1834 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9939 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': 17, 'rna3p_pur': 220, 'rna3p_pyr': 157} Link IDs: {'rna2p': 40, 'rna3p': 376} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' MG': 29} Classifications: {'undetermined': 29, 'water': 1} Link IDs: {None: 29} Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9939 At special positions: 0 Unit cell: (117.12, 164.7, 149.328, 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 29 11.99 O 3052 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: 0.52 Conformation dependent library (CDL) restraints added in 53.4 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: 5 helices and 1 sheets defined 48.3% alpha, 14.7% beta 134 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 19 removed outlier: 4.041A pdb=" N PHE B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 70 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.522A pdb=" N GLU B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.724A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.622A pdb=" N PHE B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.73 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: 1178 1.33 - 1.45: 5207 1.45 - 1.57: 3777 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" C8 G A 190 " pdb=" N7 G A 190 " ideal model delta sigma weight residual 1.305 1.290 0.015 6.00e-03 2.78e+04 6.67e+00 bond pdb=" N7 G A 190 " pdb=" C5 G A 190 " ideal model delta sigma weight residual 1.388 1.374 0.014 6.00e-03 2.78e+04 5.57e+00 bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 1.374 0.014 6.00e-03 2.78e+04 5.15e+00 bond pdb=" N9 G A 317 " pdb=" C4 G A 317 " ideal model delta sigma weight residual 1.375 1.392 -0.017 8.00e-03 1.56e+04 4.38e+00 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 3.95e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 16929 5.94 - 11.88: 10 11.88 - 17.82: 1 17.82 - 23.76: 1 23.76 - 29.70: 3 Bond angle restraints: 16944 Sorted by residual: angle pdb=" O3' A A 189 " pdb=" P G A 190 " pdb=" OP1 G A 190 " ideal model delta sigma weight residual 108.00 78.30 29.70 3.00e+00 1.11e-01 9.80e+01 angle pdb=" O3' G A 192 " pdb=" P C A 193 " pdb=" OP1 C A 193 " ideal model delta sigma weight residual 108.00 81.32 26.68 3.00e+00 1.11e-01 7.91e+01 angle pdb=" O3' G A 192 " pdb=" P C A 193 " pdb=" OP2 C A 193 " ideal model delta sigma weight residual 108.00 83.94 24.06 3.00e+00 1.11e-01 6.43e+01 angle pdb=" O3' A A 189 " pdb=" P G A 190 " pdb=" OP2 G A 190 " ideal model delta sigma weight residual 108.00 87.02 20.98 3.00e+00 1.11e-01 4.89e+01 angle pdb=" O2 C A 119 " pdb=" C2 C A 119 " pdb=" N3 C A 119 " ideal model delta sigma weight residual 121.90 117.25 4.65 7.00e-01 2.04e+00 4.41e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 5888 33.64 - 67.29: 1071 67.29 - 100.93: 146 100.93 - 134.58: 3 134.58 - 168.22: 8 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 -160.00 -59.82 -100.18 1 1.50e+01 4.44e-03 5.02e+01 dihedral pdb=" O4' U A 371 " pdb=" C1' U A 371 " pdb=" N1 U A 371 " pdb=" C2 U A 371 " ideal model delta sinusoidal sigma weight residual -160.00 -69.36 -90.64 1 1.50e+01 4.44e-03 4.31e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -160.00 -87.05 -72.95 1 1.50e+01 4.44e-03 3.02e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 2219 0.409 - 0.817: 0 0.817 - 1.226: 0 1.226 - 1.634: 0 1.634 - 2.043: 2 Chirality restraints: 2221 Sorted by residual: chirality pdb=" P G A 190 " pdb=" OP1 G A 190 " pdb=" OP2 G A 190 " pdb=" O5' G A 190 " both_signs ideal model delta sigma weight residual True 2.41 0.37 2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" P C A 193 " pdb=" OP1 C A 193 " pdb=" OP2 C A 193 " pdb=" O5' C A 193 " both_signs ideal model delta sigma weight residual True 2.41 0.45 1.96 2.00e-01 2.50e+01 9.60e+01 chirality pdb=" CA GLN B 18 " pdb=" N GLN B 18 " pdb=" C GLN B 18 " pdb=" CB GLN B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 119 " 0.006 2.00e-02 2.50e+03 2.43e-02 1.33e+01 pdb=" N1 C A 119 " -0.008 2.00e-02 2.50e+03 pdb=" C2 C A 119 " 0.059 2.00e-02 2.50e+03 pdb=" O2 C A 119 " -0.038 2.00e-02 2.50e+03 pdb=" N3 C A 119 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C A 119 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C A 119 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C A 119 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C A 119 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 18 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" CD GLN B 18 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLN B 18 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN B 18 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 133 " -0.003 2.00e-02 2.50e+03 1.48e-02 6.57e+00 pdb=" N9 G A 133 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 133 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A 133 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G A 133 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A 133 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G A 133 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A 133 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 133 " 0.040 2.00e-02 2.50e+03 pdb=" N2 G A 133 " -0.026 2.00e-02 2.50e+03 pdb=" N3 G A 133 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 133 " -0.008 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.11: 6870 3.11 - 3.70: 21527 3.70 - 4.30: 28094 4.30 - 4.90: 35353 Nonbonded interactions: 91884 Sorted by model distance: nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 511 " model vdw 1.910 2.170 nonbonded pdb=" OP2 C A 258 " pdb="MG MG A 508 " model vdw 1.956 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 511 " model vdw 1.969 2.170 nonbonded pdb=" OP2 G A 331 " pdb="MG MG A 511 " model vdw 1.975 2.170 nonbonded pdb=" OP1 A A 50 " pdb="MG MG A 504 " model vdw 1.987 2.170 ... (remaining 91879 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: 9.340 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.004 0.040 11000 Z= 0.349 Angle : 0.974 29.697 16944 Z= 0.759 Chirality : 0.088 2.043 2221 Planarity : 0.004 0.027 581 Dihedral : 25.860 168.220 6900 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % Rotamer: Outliers : 4.04 % Allowed : 36.36 % 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: -0.25 (0.86), residues: 114 helix: 1.69 (0.85), residues: 45 sheet: 0.17 (1.02), residues: 28 loop : -2.64 (1.01), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.016 0.002 TYR B 63 PHE 0.015 0.002 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.35 (11000) covalent geometry : angle 0.97374 / 0.76 (16944) hydrogen bonds : bond 0.10136 / 11.28 ( 390) hydrogen bonds : angle 3.79600 / 5.70 ( 721) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.131 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 22 average time/residue: 0.0702 time to fit residues: 2.3282 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 68 PHE 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: 6.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.070050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043760 restraints weight = 78545.949| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.05 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 11000 Z= 0.524 Angle : 1.103 29.813 16944 Z= 0.533 Chirality : 0.089 1.945 2221 Planarity : 0.007 0.049 581 Dihedral : 26.173 177.926 6653 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 37.53 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Rotamer: Outliers : 12.12 % Allowed : 25.25 % Favored : 62.63 % 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: -1.34 (0.80), residues: 114 helix: 0.45 (0.80), residues: 46 sheet: -0.77 (0.92), residues: 28 loop : -2.55 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG B 106 TYR 0.016 0.003 TYR B 31 PHE 0.026 0.004 PHE B 13 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.52 (11000) covalent geometry : angle 1.10287 / 0.53 (16944) hydrogen bonds : bond 0.13000 / 13.83 ( 390) hydrogen bonds : angle 3.46424 / 4.59 ( 721) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.103 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 25 average time/residue: 0.0794 time to fit residues: 2.8820 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 18 GLN 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 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 overall best weight: 7.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.069022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038526 restraints weight = 79505.725| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.78 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11000 Z= 0.463 Angle : 1.067 29.816 16944 Z= 0.528 Chirality : 0.087 1.965 2221 Planarity : 0.007 0.036 581 Dihedral : 26.679 167.417 6651 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 41.54 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Rotamer: Outliers : 13.13 % Allowed : 26.26 % 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: -1.82 (0.76), residues: 114 helix: 0.07 (0.80), residues: 46 sheet: -1.14 (0.85), residues: 28 loop : -2.72 (0.91), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.013 0.003 TYR B 63 PHE 0.017 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.46 (11000) covalent geometry : angle 1.06707 / 0.53 (16944) hydrogen bonds : bond 0.13390 / 14.64 ( 390) hydrogen bonds : angle 3.45930 / 4.48 ( 721) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.125 Fit side-chains REVERT: B 74 GLU cc_start: 0.9356 (tp30) cc_final: 0.9101 (tp30) outliers start: 13 outliers final: 10 residues processed: 25 average time/residue: 0.0936 time to fit residues: 3.4501 Evaluate side-chains 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 47 VAL 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 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.069530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.039664 restraints weight = 79152.849| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.85 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11000 Z= 0.304 Angle : 0.867 29.962 16944 Z= 0.436 Chirality : 0.077 1.915 2221 Planarity : 0.006 0.024 581 Dihedral : 26.545 170.015 6648 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 31.77 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.89 % Favored : 91.23 % Rotamer: Outliers : 11.11 % Allowed : 27.27 % Favored : 61.62 % 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: -1.37 (0.78), residues: 114 helix: 0.49 (0.79), residues: 46 sheet: -0.98 (0.86), residues: 28 loop : -2.47 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 57 TYR 0.014 0.002 TYR B 63 PHE 0.026 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.30 (11000) covalent geometry : angle 0.86688 / 0.44 (16944) hydrogen bonds : bond 0.11343 / 12.28 ( 390) hydrogen bonds : angle 3.21538 / 4.20 ( 721) *********************** 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 31 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.090 Fit side-chains REVERT: B 74 GLU cc_start: 0.9394 (tp30) cc_final: 0.9087 (tp30) outliers start: 11 outliers final: 9 residues processed: 25 average time/residue: 0.0739 time to fit residues: 2.6371 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.067868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041989 restraints weight = 79789.402| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.07 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 11000 Z= 0.618 Angle : 1.290 31.125 16944 Z= 0.615 Chirality : 0.096 1.850 2221 Planarity : 0.008 0.047 581 Dihedral : 26.895 170.337 6648 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 52.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 13.13 % Allowed : 22.22 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.76), residues: 114 helix: -0.45 (0.78), residues: 46 sheet: -1.68 (0.81), residues: 28 loop : -2.79 (0.98), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.013 0.003 TYR B 40 PHE 0.022 0.004 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.62 (11000) covalent geometry : angle 1.29021 / 0.61 (16944) hydrogen bonds : bond 0.16277 / 17.68 ( 390) hydrogen bonds : angle 3.93135 / 5.14 ( 721) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 16 time to evaluate : 0.087 Fit side-chains REVERT: B 4 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8803 (ttmm) REVERT: B 19 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8606 (mp10) REVERT: B 74 GLU cc_start: 0.9331 (tp30) cc_final: 0.9123 (tp30) outliers start: 13 outliers final: 11 residues processed: 23 average time/residue: 0.0910 time to fit residues: 2.9329 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 16 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 47 VAL 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 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 50.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.069400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.039316 restraints weight = 78563.423| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.50 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11000 Z= 0.227 Angle : 0.812 29.676 16944 Z= 0.419 Chirality : 0.075 1.918 2221 Planarity : 0.005 0.025 581 Dihedral : 26.686 169.374 6648 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 29.63 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.60 % Rotamer: Outliers : 11.11 % Allowed : 22.22 % 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: -1.23 (0.77), residues: 114 helix: 0.75 (0.79), residues: 46 sheet: -1.07 (0.84), residues: 28 loop : -2.46 (0.96), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.013 0.002 TYR B 63 PHE 0.013 0.002 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.23 (11000) covalent geometry : angle 0.81166 / 0.42 (16944) hydrogen bonds : bond 0.11426 / 12.43 ( 390) hydrogen bonds : angle 3.13454 / 4.04 ( 721) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 time to evaluate : 0.138 Fit side-chains REVERT: B 4 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8751 (mttp) REVERT: B 74 GLU cc_start: 0.9317 (tp30) cc_final: 0.9041 (tp30) outliers start: 11 outliers final: 7 residues processed: 23 average time/residue: 0.0932 time to fit residues: 3.0598 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.068646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042638 restraints weight = 79210.235| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.07 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3913 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= 0.393 Angle : 0.929 30.152 16944 Z= 0.465 Chirality : 0.080 1.899 2221 Planarity : 0.006 0.029 581 Dihedral : 26.676 168.610 6648 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 35.84 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.40 % Favored : 87.72 % Rotamer: Outliers : 13.13 % Allowed : 21.21 % 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: -1.45 (0.77), residues: 114 helix: 0.43 (0.78), residues: 46 sheet: -1.16 (0.84), residues: 28 loop : -2.40 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 106 TYR 0.009 0.002 TYR B 63 PHE 0.011 0.002 PHE B 13 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.39 (11000) covalent geometry : angle 0.92906 / 0.46 (16944) hydrogen bonds : bond 0.12414 / 13.48 ( 390) hydrogen bonds : angle 3.33345 / 4.36 ( 721) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.087 Fit side-chains REVERT: B 4 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8690 (ttmm) REVERT: B 74 GLU cc_start: 0.9357 (tp30) cc_final: 0.9105 (tp30) outliers start: 13 outliers final: 9 residues processed: 26 average time/residue: 0.0903 time to fit residues: 3.3380 Evaluate side-chains 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 10 optimal weight: 10.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.067127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037133 restraints weight = 77255.977| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.11 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.105 11000 Z= 0.640 Angle : 1.330 31.270 16944 Z= 0.634 Chirality : 0.097 1.816 2221 Planarity : 0.009 0.047 581 Dihedral : 27.035 170.888 6648 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 56.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 10.10 % Allowed : 25.25 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.73), residues: 114 helix: -0.74 (0.75), residues: 46 sheet: -1.91 (0.81), residues: 28 loop : -3.02 (0.94), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 59 TYR 0.014 0.003 TYR B 40 PHE 0.017 0.003 PHE B 13 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.64 (11000) covalent geometry : angle 1.32978 / 0.63 (16944) hydrogen bonds : bond 0.16986 / 18.55 ( 390) hydrogen bonds : angle 4.06073 / 5.31 ( 721) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.090 Fit side-chains REVERT: B 4 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (ttmm) REVERT: B 96 GLU cc_start: 0.8897 (mp0) cc_final: 0.8399 (pm20) outliers start: 10 outliers final: 7 residues processed: 21 average time/residue: 0.1004 time to fit residues: 3.0849 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 27 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.067957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041412 restraints weight = 77769.379| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.07 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11000 Z= 0.379 Angle : 1.002 30.137 16944 Z= 0.498 Chirality : 0.083 1.854 2221 Planarity : 0.007 0.035 581 Dihedral : 26.870 169.868 6648 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 39.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % 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: -2.06 (0.77), residues: 114 helix: -0.07 (0.78), residues: 46 sheet: -1.51 (0.82), residues: 28 loop : -2.71 (1.00), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.009 0.002 TYR B 31 PHE 0.013 0.002 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.38 (11000) covalent geometry : angle 1.00170 / 0.50 (16944) hydrogen bonds : bond 0.13264 / 14.58 ( 390) hydrogen bonds : angle 3.54926 / 4.58 ( 721) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.090 Fit side-chains REVERT: B 4 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8699 (ttmm) outliers start: 9 outliers final: 8 residues processed: 24 average time/residue: 0.0921 time to fit residues: 2.9859 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 overall best weight: 7.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.067539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036672 restraints weight = 76160.494| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.01 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 11000 Z= 0.495 Angle : 1.123 30.392 16944 Z= 0.544 Chirality : 0.089 1.851 2221 Planarity : 0.007 0.041 581 Dihedral : 26.870 169.433 6648 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 44.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 9.09 % Allowed : 27.27 % 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: -2.32 (0.76), residues: 114 helix: -0.46 (0.76), residues: 46 sheet: -1.67 (0.80), residues: 28 loop : -2.58 (1.03), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 106 TYR 0.008 0.003 TYR B 31 PHE 0.010 0.003 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.49 (11000) covalent geometry : angle 1.12277 / 0.54 (16944) hydrogen bonds : bond 0.13919 / 15.25 ( 390) hydrogen bonds : angle 3.81204 / 5.13 ( 721) ********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.116 Fit side-chains REVERT: B 4 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8895 (ttmm) REVERT: B 96 GLU cc_start: 0.8886 (mp0) cc_final: 0.8384 (pm20) outliers start: 9 outliers final: 7 residues processed: 21 average time/residue: 0.1047 time to fit residues: 3.0503 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.069346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.039479 restraints weight = 78974.842| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.50 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11000 Z= 0.182 Angle : 0.792 29.091 16944 Z= 0.407 Chirality : 0.072 1.924 2221 Planarity : 0.005 0.026 581 Dihedral : 26.629 166.971 6648 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.60 % 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: -1.15 (0.76), residues: 114 helix: 0.65 (0.74), residues: 46 sheet: -0.91 (0.84), residues: 28 loop : -2.29 (0.99), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.013 0.002 TYR B 31 PHE 0.009 0.002 PHE B 28 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.18 (11000) covalent geometry : angle 0.79185 / 0.41 (16944) hydrogen bonds : bond 0.10564 / 11.54 ( 390) hydrogen bonds : angle 3.07778 / 3.96 ( 721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.55 seconds wall clock time: 37 minutes 47.73 seconds (2267.73 seconds total)