Starting phenix.real_space_refine on Fri Jul 3 02:49:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oww_70946/07_2026/9oww_70946.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 29 9.91 5 P 500 5.49 5 S 3 5.16 5 C 5391 2.51 5 N 2143 2.21 5 O 3637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11703 Number of models: 1 Model: "" Number of chains: 4 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': 15, 'rna3p_pur': 218, 'rna3p_pyr': 159} 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: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1765 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 31, 'rna3p_pyr': 35} Link IDs: {'rna2p': 16, 'rna3p': 66} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 0 Ad-hoc single atom residues: {' CA': 29} Chain breaks: 29 Time building chain proxies: 3.28, per 1000 atoms: 0.28 Number of scatterers: 11703 At special positions: 0 Unit cell: (126.49, 141.005, 174.182, 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) Ca 29 19.99 S 3 16.00 P 500 15.00 O 3637 8.00 N 2143 7.00 C 5391 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: 1.10 Conformation dependent library (CDL) restraints added in 88.1 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, 16.4% beta 168 base pairs and 292 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.708A 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 24 removed outlier: 6.091A pdb=" N ARG B 42 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE B 83 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 47 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 427 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 168 basepair parallelities 292 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1081 1.32 - 1.44: 6212 1.44 - 1.56: 4675 1.56 - 1.68: 997 1.68 - 1.80: 5 Bond restraints: 12970 Sorted by residual: bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.14e+01 bond pdb=" N LEU B 111 " pdb=" CA LEU B 111 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" N VAL B 97 " pdb=" CA VAL B 97 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.66e+00 bond pdb=" N GLY B 93 " pdb=" CA GLY B 93 " ideal model delta sigma weight residual 1.450 1.478 -0.028 1.04e-02 9.25e+03 7.21e+00 bond pdb=" C ARG B 59 " pdb=" O ARG B 59 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.22e-02 6.72e+03 6.48e+00 ... (remaining 12965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 18467 2.93 - 5.86: 1315 5.86 - 8.79: 219 8.79 - 11.72: 8 11.72 - 14.64: 3 Bond angle restraints: 20012 Sorted by residual: angle pdb=" O3' C A 405 " pdb=" P A A 406 " pdb=" O5' A A 406 " ideal model delta sigma weight residual 104.00 95.09 8.91 1.50e+00 4.44e-01 3.53e+01 angle pdb=" C4' C A 182 " pdb=" C3' C A 182 " pdb=" C2' C A 182 " ideal model delta sigma weight residual 102.60 96.71 5.89 1.00e+00 1.00e+00 3.47e+01 angle pdb=" O3' G A 149 " pdb=" P A A 150 " pdb=" O5' A A 150 " ideal model delta sigma weight residual 104.00 95.44 8.56 1.50e+00 4.44e-01 3.25e+01 angle pdb=" O3' U C 46 " pdb=" C3' U C 46 " pdb=" C2' U C 46 " ideal model delta sigma weight residual 109.50 117.82 -8.32 1.50e+00 4.44e-01 3.08e+01 angle pdb=" O3' U A 67 " pdb=" P G A 68 " pdb=" O5' G A 68 " ideal model delta sigma weight residual 104.00 95.88 8.12 1.50e+00 4.44e-01 2.93e+01 ... (remaining 20007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 6855 35.94 - 71.88: 1386 71.88 - 107.82: 179 107.82 - 143.76: 5 143.76 - 179.70: 6 Dihedral angle restraints: 8431 sinusoidal: 8094 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 16.24 -176.24 1 1.50e+01 4.44e-03 8.52e+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 52.40 179.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 329 " pdb=" C1' U A 329 " pdb=" N1 U A 329 " pdb=" C2 U A 329 " ideal model delta sinusoidal sigma weight residual 232.00 58.51 173.49 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 8428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1874 0.122 - 0.244: 418 0.244 - 0.365: 79 0.365 - 0.487: 239 0.487 - 0.609: 26 Chirality restraints: 2636 Sorted by residual: chirality pdb=" P U A 267 " pdb=" OP1 U A 267 " pdb=" OP2 U A 267 " pdb=" O5' U A 267 " both_signs ideal model delta sigma weight residual True 2.41 -3.02 -0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" P A C 75 " pdb=" OP1 A C 75 " pdb=" OP2 A C 75 " pdb=" O5' A C 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 2633 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.414 9.50e-02 1.11e+02 1.86e-01 2.11e+01 pdb=" NE ARG B 59 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 299 " -0.050 2.00e-02 2.50e+03 2.04e-02 1.25e+01 pdb=" N9 G A 299 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G A 299 " 0.011 2.00e-02 2.50e+03 pdb=" N7 G A 299 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 299 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 299 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G A 299 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G A 299 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G A 299 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G A 299 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A 299 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G A 299 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 318 " -0.033 2.00e-02 2.50e+03 1.62e-02 5.91e+00 pdb=" N1 C A 318 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C A 318 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C A 318 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C A 318 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C A 318 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C A 318 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C A 318 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A 318 " 0.010 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 9 2.05 - 2.76: 2449 2.76 - 3.47: 15774 3.47 - 4.19: 44996 4.19 - 4.90: 51874 Nonbonded interactions: 115102 Sorted by model distance: nonbonded pdb=" OP2 A A 364 " pdb=" C8 G A 365 " model vdw 1.337 3.260 nonbonded pdb=" O3' A A 363 " pdb=" C8 A A 364 " model vdw 1.361 3.260 nonbonded pdb=" C3' A A 363 " pdb=" C8 A A 364 " model vdw 1.368 3.690 nonbonded pdb=" O6 G A 230 " pdb="CA CA A 529 " model vdw 1.748 3.250 nonbonded pdb=" OP2 A A 364 " pdb=" N9 G A 365 " model vdw 1.836 3.120 ... (remaining 115097 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: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.009 0.044 12970 Z= 0.638 Angle : 1.585 14.644 20012 Z= 0.923 Chirality : 0.168 0.609 2636 Planarity : 0.008 0.186 664 Dihedral : 27.592 179.701 8215 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 26.26 % Favored : 68.69 % 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: 1.49 (0.81), residues: 114 helix: 1.98 (0.83), residues: 46 sheet: 0.86 (0.82), residues: 29 loop : -0.02 (1.09), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.009 0.001 TYR B 94 PHE 0.004 0.001 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.64 (12970) covalent geometry : angle 1.58466 / 0.92 (20012) hydrogen bonds : bond 0.18738 / 18.28 ( 474) hydrogen bonds : angle 9.40730 / 12.22 ( 857) *********************** 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 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.184 Fit side-chains REVERT: B 12 GLU cc_start: 0.8905 (mp0) cc_final: 0.8651 (mt-10) REVERT: B 71 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8677 (pp) outliers start: 5 outliers final: 0 residues processed: 35 average time/residue: 0.6825 time to fit residues: 25.7022 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN B 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.077988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.046641 restraints weight = 49743.114| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.92 r_work: 0.2800 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 12970 Z= 0.495 Angle : 0.758 12.435 20012 Z= 0.447 Chirality : 0.054 0.320 2636 Planarity : 0.007 0.030 664 Dihedral : 26.773 179.680 7962 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 11.11 % Allowed : 21.21 % 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: 0.93 (0.78), residues: 114 helix: 1.08 (0.74), residues: 54 sheet: 0.84 (0.67), residues: 29 loop : -0.24 (1.31), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 26 TYR 0.008 0.002 TYR B 40 PHE 0.013 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.49 (12970) covalent geometry : angle 0.75828 / 0.45 (20012) hydrogen bonds : bond 0.11596 / 12.05 ( 474) hydrogen bonds : angle 2.75402 / 3.17 ( 857) *********************** 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.161 Fit side-chains REVERT: B 12 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: B 26 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8433 (ttm170) REVERT: B 69 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9044 (tp) outliers start: 11 outliers final: 3 residues processed: 27 average time/residue: 0.8916 time to fit residues: 25.5324 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.077806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.046606 restraints weight = 50042.452| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.77 r_work: 0.2814 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 12970 Z= 0.465 Angle : 0.676 10.892 20012 Z= 0.406 Chirality : 0.048 0.252 2636 Planarity : 0.006 0.043 664 Dihedral : 26.629 178.083 7962 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 10.10 % Allowed : 19.19 % 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: 0.16 (0.76), residues: 114 helix: 0.86 (0.72), residues: 48 sheet: 0.36 (0.74), residues: 29 loop : -0.98 (1.14), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 86 TYR 0.014 0.003 TYR B 40 PHE 0.015 0.003 PHE B 68 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.47 (12970) covalent geometry : angle 0.67585 / 0.41 (20012) hydrogen bonds : bond 0.10989 / 11.39 ( 474) hydrogen bonds : angle 2.83138 / 3.33 ( 857) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.160 Fit side-chains REVERT: B 6 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: B 12 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: B 35 ARG cc_start: 0.8381 (mmt90) cc_final: 0.8109 (mmt180) REVERT: B 38 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8019 (tt0) outliers start: 10 outliers final: 3 residues processed: 26 average time/residue: 0.8544 time to fit residues: 23.5278 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.077999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.046907 restraints weight = 49740.739| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.35 r_work: 0.2833 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12970 Z= 0.328 Angle : 0.558 7.022 20012 Z= 0.349 Chirality : 0.041 0.247 2636 Planarity : 0.005 0.034 664 Dihedral : 26.488 176.018 7962 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 0.21 (0.77), residues: 114 helix: 1.62 (0.75), residues: 47 sheet: -0.08 (0.75), residues: 29 loop : -1.57 (1.07), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.010 0.002 TYR B 40 PHE 0.012 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.33 (12970) covalent geometry : angle 0.55829 / 0.35 (20012) hydrogen bonds : bond 0.08343 / 8.70 ( 474) hydrogen bonds : angle 2.45445 / 2.78 ( 857) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.139 Fit side-chains REVERT: B 12 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8668 (mt-10) outliers start: 9 outliers final: 2 residues processed: 25 average time/residue: 0.7196 time to fit residues: 19.2294 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.077217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.046131 restraints weight = 49749.502| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.76 r_work: 0.2809 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12970 Z= 0.429 Angle : 0.635 7.608 20012 Z= 0.385 Chirality : 0.046 0.256 2636 Planarity : 0.006 0.026 664 Dihedral : 26.351 176.353 7960 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.84 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: 0.33 (0.81), residues: 114 helix: 1.47 (0.75), residues: 47 sheet: -0.00 (0.82), residues: 29 loop : -1.13 (1.20), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 35 TYR 0.010 0.002 TYR B 40 PHE 0.013 0.002 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.43 (12970) covalent geometry : angle 0.63514 / 0.38 (20012) hydrogen bonds : bond 0.10097 / 10.37 ( 474) hydrogen bonds : angle 2.55255 / 2.92 ( 857) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.156 Fit side-chains REVERT: B 6 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8141 (mtp180) REVERT: B 12 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8712 (mt-10) outliers start: 9 outliers final: 5 residues processed: 24 average time/residue: 0.8215 time to fit residues: 20.8929 Evaluate side-chains 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 40.0000 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.077179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045900 restraints weight = 49705.238| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.30 r_work: 0.2818 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.090 12970 Z= 0.633 Angle : 0.769 9.407 20012 Z= 0.453 Chirality : 0.056 0.261 2636 Planarity : 0.007 0.029 664 Dihedral : 26.360 177.011 7960 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 10.10 % Allowed : 22.22 % 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: -0.06 (0.81), residues: 114 helix: 1.12 (0.73), residues: 47 sheet: -0.09 (0.87), residues: 29 loop : -1.38 (1.21), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.010 0.003 TYR B 40 PHE 0.013 0.003 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01038 / 0.63 (12970) covalent geometry : angle 0.76944 / 0.45 (20012) hydrogen bonds : bond 0.11620 / 12.07 ( 474) hydrogen bonds : angle 2.66870 / 3.05 ( 857) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.097 Fit side-chains REVERT: B 6 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8080 (mtp180) REVERT: B 12 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: B 35 ARG cc_start: 0.8551 (mmt90) cc_final: 0.8307 (mmt-90) REVERT: B 96 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8021 (pt0) outliers start: 10 outliers final: 3 residues processed: 23 average time/residue: 0.8640 time to fit residues: 21.0073 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 overall best weight: 4.3590 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.078103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047663 restraints weight = 49222.521| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.59 r_work: 0.2905 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12970 Z= 0.431 Angle : 0.625 7.296 20012 Z= 0.381 Chirality : 0.046 0.257 2636 Planarity : 0.006 0.031 664 Dihedral : 26.364 175.770 7960 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.67 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: 0.09 (0.80), residues: 114 helix: 1.43 (0.74), residues: 47 sheet: -0.28 (0.85), residues: 29 loop : -1.35 (1.16), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.009 0.002 TYR B 31 PHE 0.016 0.003 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.43 (12970) covalent geometry : angle 0.62514 / 0.38 (20012) hydrogen bonds : bond 0.09190 / 9.44 ( 474) hydrogen bonds : angle 2.50995 / 2.88 ( 857) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.134 Fit side-chains REVERT: B 6 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8278 (mtp180) REVERT: B 12 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8717 (mt-10) REVERT: B 35 ARG cc_start: 0.8523 (mmt90) cc_final: 0.8242 (mmt180) outliers start: 8 outliers final: 2 residues processed: 23 average time/residue: 0.8759 time to fit residues: 21.3680 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.076854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045703 restraints weight = 49513.764| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.34 r_work: 0.2809 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.089 12970 Z= 0.657 Angle : 0.798 9.167 20012 Z= 0.470 Chirality : 0.057 0.263 2636 Planarity : 0.007 0.038 664 Dihedral : 26.345 176.587 7960 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 10.10 % Allowed : 23.23 % 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: -0.27 (0.81), residues: 114 helix: 0.93 (0.72), residues: 47 sheet: -0.17 (0.92), residues: 29 loop : -1.52 (1.18), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.012 0.002 TYR B 40 PHE 0.011 0.003 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01076 / 0.66 (12970) covalent geometry : angle 0.79829 / 0.47 (20012) hydrogen bonds : bond 0.12641 / 13.06 ( 474) hydrogen bonds : angle 2.76707 / 3.14 ( 857) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.098 Fit side-chains REVERT: B 6 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8082 (mtp180) REVERT: B 12 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8687 (mt-10) outliers start: 10 outliers final: 3 residues processed: 23 average time/residue: 0.9140 time to fit residues: 22.1611 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.077853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047191 restraints weight = 49421.814| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.91 r_work: 0.2845 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12970 Z= 0.232 Angle : 0.534 7.499 20012 Z= 0.335 Chirality : 0.037 0.263 2636 Planarity : 0.005 0.027 664 Dihedral : 26.341 175.312 7960 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 6.06 % Allowed : 27.27 % 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: 0.34 (0.81), residues: 114 helix: 1.83 (0.79), residues: 47 sheet: -0.31 (0.83), residues: 29 loop : -1.37 (1.08), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.012 0.002 TYR B 94 PHE 0.016 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.23 (12970) covalent geometry : angle 0.53428 / 0.34 (20012) hydrogen bonds : bond 0.07442 / 7.54 ( 474) hydrogen bonds : angle 2.43998 / 2.78 ( 857) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.172 Fit side-chains REVERT: B 6 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8092 (mtp180) REVERT: B 12 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8677 (mt-10) outliers start: 6 outliers final: 1 residues processed: 23 average time/residue: 0.8744 time to fit residues: 21.3396 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.077007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045850 restraints weight = 49773.264| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.04 r_work: 0.2819 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 12970 Z= 0.580 Angle : 0.726 8.020 20012 Z= 0.431 Chirality : 0.053 0.260 2636 Planarity : 0.007 0.033 664 Dihedral : 26.221 176.312 7960 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % 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: -0.06 (0.81), residues: 114 helix: 1.33 (0.77), residues: 47 sheet: -0.31 (0.87), residues: 29 loop : -1.52 (1.13), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 26 TYR 0.011 0.002 TYR B 40 PHE 0.011 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00951 / 0.58 (12970) covalent geometry : angle 0.72563 / 0.43 (20012) hydrogen bonds : bond 0.10822 / 11.03 ( 474) hydrogen bonds : angle 2.65473 / 3.01 ( 857) ********************** 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 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.144 Fit side-chains REVERT: B 6 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8069 (mtp180) REVERT: B 12 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8620 (mt-10) outliers start: 4 outliers final: 1 residues processed: 21 average time/residue: 0.9779 time to fit residues: 21.6701 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 99 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.077789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046825 restraints weight = 49867.941| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 0.96 r_work: 0.2839 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12970 Z= 0.241 Angle : 0.520 7.806 20012 Z= 0.328 Chirality : 0.037 0.268 2636 Planarity : 0.005 0.030 664 Dihedral : 26.246 175.400 7960 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.04 % Allowed : 31.31 % 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: 0.14 (0.81), residues: 114 helix: 1.75 (0.79), residues: 47 sheet: -0.77 (0.83), residues: 31 loop : -1.26 (1.10), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 26 TYR 0.013 0.002 TYR B 31 PHE 0.012 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.24 (12970) covalent geometry : angle 0.52027 / 0.33 (20012) hydrogen bonds : bond 0.07317 / 7.38 ( 474) hydrogen bonds : angle 2.44208 / 2.77 ( 857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.96 seconds wall clock time: 82 minutes 9.91 seconds (4929.91 seconds total)