Starting phenix.real_space_refine on Wed Aug 5 20:46:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oww_70946/08_2026/9oww_70946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oww_70946/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9oww_70946/08_2026/9oww_70946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oww_70946/08_2026/9oww_70946.map" model { file = "/net/cci-nas-00/data/ceres_data/9oww_70946/08_2026/9oww_70946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oww_70946/08_2026/9oww_70946_neut.cif" } 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-2.2rc3-6140/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, 29 Unusual residues: {' CA': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Time building chain proxies: 2.53, per 1000 atoms: 0.22 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: 0.67 Conformation dependent library (CDL) restraints added in 56.2 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: 1.65 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: 2.70 Time building geometry restraints manager: 0.94 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=" P A C 20 " pdb=" O5' A C 20 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 9.22e+00 bond pdb=" P U A 267 " pdb=" O5' U A 267 " ideal model delta sigma weight residual 1.593 1.623 -0.030 1.00e-02 1.00e+04 9.20e+00 bond pdb=" P A A 50 " pdb=" O5' A A 50 " ideal model delta sigma weight residual 1.593 1.564 0.029 1.00e-02 1.00e+04 8.54e+00 ... (remaining 12965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 18582 2.93 - 5.86: 1195 5.86 - 8.79: 224 8.79 - 11.72: 8 11.72 - 14.64: 3 Bond angle restraints: 20012 Sorted by residual: 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=" C4' G C 44 " pdb=" O4' G C 44 " pdb=" C1' G C 44 " ideal model delta sigma weight residual 109.70 106.01 3.69 7.00e-01 2.04e+00 2.79e+01 angle pdb=" C4' A A 240 " pdb=" C3' A A 240 " pdb=" C2' A A 240 " ideal model delta sigma weight residual 102.60 97.56 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" C4' C A 176 " pdb=" C3' C A 176 " pdb=" C2' C A 176 " ideal model delta sigma weight residual 102.60 97.62 4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" C3' C A 159 " pdb=" C2' C A 159 " pdb=" C1' C A 159 " ideal model delta sigma weight residual 101.30 104.76 -3.46 7.00e-01 2.04e+00 2.45e+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: 1828 0.122 - 0.244: 464 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 2.510 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: 4.150 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.860 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- 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= 0.701 Angle : 1.581 14.644 20012 Z= 0.931 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 0.00919 / 0.70 (12970) covalent geometry : angle 1.58086 / 0.93 (20012) hydrogen bonds : bond 0.18738 / 20.37 ( 474) hydrogen bonds : angle 9.40730 / 12.96 ( 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 : 0.150 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: 0.6015 time to fit residues: 22.7567 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 : 0.155 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.077805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.046948 restraints weight = 49646.071| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.50 r_work: 0.2789 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 12970 Z= 0.517 Angle : 0.931 14.383 20012 Z= 0.480 Chirality : 0.066 0.366 2636 Planarity : 0.007 0.023 664 Dihedral : 26.678 175.869 7962 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 12.12 % Allowed : 20.20 % 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: 0.80 (0.77), residues: 114 helix: 1.00 (0.73), residues: 54 sheet: 0.79 (0.66), residues: 29 loop : -0.37 (1.28), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.009 0.002 TYR B 40 PHE 0.011 0.003 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.52 (12970) covalent geometry : angle 0.93089 / 0.48 (20012) hydrogen bonds : bond 0.11959 / 13.53 ( 474) hydrogen bonds : angle 2.85308 / 3.63 ( 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: 12 poor density : 20 time to evaluate : 0.155 Fit side-chains REVERT: B 12 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8627 (mt-10) REVERT: B 26 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8052 (ttm-80) outliers start: 12 outliers final: 4 residues processed: 27 average time/residue: 0.7586 time to fit residues: 21.7717 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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 32 THR 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: 50.0000 chunk 56 optimal weight: 50.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 overall best weight: 5.5786 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.077674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046142 restraints weight = 50044.289| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.29 r_work: 0.2806 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 12970 Z= 0.487 Angle : 0.867 10.720 20012 Z= 0.452 Chirality : 0.059 0.389 2636 Planarity : 0.007 0.043 664 Dihedral : 26.559 178.152 7962 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 11.11 % Allowed : 18.18 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.76), residues: 114 helix: 0.89 (0.73), residues: 47 sheet: 0.22 (0.79), residues: 29 loop : -1.23 (1.10), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 26 TYR 0.018 0.004 TYR B 40 PHE 0.015 0.003 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.49 (12970) covalent geometry : angle 0.86710 / 0.45 (20012) hydrogen bonds : bond 0.11630 / 13.22 ( 474) hydrogen bonds : angle 2.91043 / 3.71 ( 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 32 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.178 Fit side-chains REVERT: B 6 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8069 (mtp180) REVERT: B 12 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: B 35 ARG cc_start: 0.8388 (mmt90) cc_final: 0.8137 (mmt-90) REVERT: B 38 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7926 (tt0) outliers start: 11 outliers final: 3 residues processed: 28 average time/residue: 0.8172 time to fit residues: 24.1850 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 : 0.157 ------------------------------------------------------------------------------- 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 34 ASP Chi-restraints excluded: chain B residue 38 GLN 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: 10.0000 chunk 15 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.077756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046318 restraints weight = 49913.505| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.09 r_work: 0.2814 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12970 Z= 0.395 Angle : 0.743 8.692 20012 Z= 0.401 Chirality : 0.052 0.372 2636 Planarity : 0.006 0.025 664 Dihedral : 26.344 178.959 7960 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 26.26 % 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: -0.02 (0.76), residues: 114 helix: 1.35 (0.74), residues: 47 sheet: -0.15 (0.79), residues: 29 loop : -1.61 (1.02), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.012 0.002 TYR B 40 PHE 0.014 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.39 (12970) covalent geometry : angle 0.74322 / 0.40 (20012) hydrogen bonds : bond 0.09560 / 10.86 ( 474) hydrogen bonds : angle 2.55831 / 3.26 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: B 35 ARG cc_start: 0.8483 (mmt90) cc_final: 0.8156 (mmt180) outliers start: 6 outliers final: 4 residues processed: 21 average time/residue: 0.7586 time to fit residues: 16.8576 Evaluate side-chains 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 34 ASP 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: 1.9990 chunk 17 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 chunk 58 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.077136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045741 restraints weight = 49837.953| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.44 r_work: 0.2796 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 12970 Z= 0.508 Angle : 0.879 8.740 20012 Z= 0.455 Chirality : 0.062 0.398 2636 Planarity : 0.007 0.031 664 Dihedral : 26.284 179.343 7960 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 22.22 % 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: -0.32 (0.77), residues: 114 helix: 0.96 (0.72), residues: 47 sheet: -0.12 (0.87), residues: 29 loop : -1.74 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 65 TYR 0.007 0.002 TYR B 5 PHE 0.013 0.003 PHE B 68 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.51 (12970) covalent geometry : angle 0.87949 / 0.45 (20012) hydrogen bonds : bond 0.11702 / 13.16 ( 474) hydrogen bonds : angle 2.72208 / 3.47 ( 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.187 Fit side-chains REVERT: B 6 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.7958 (mtp180) REVERT: B 12 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8585 (mt-10) outliers start: 7 outliers final: 6 residues processed: 23 average time/residue: 0.8855 time to fit residues: 21.4660 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 : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 99 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 50.0000 chunk 35 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 7.3792 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.076533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.045425 restraints weight = 50055.628| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.74 r_work: 0.2775 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.095 12970 Z= 0.655 Angle : 1.088 10.548 20012 Z= 0.538 Chirality : 0.074 0.394 2636 Planarity : 0.008 0.034 664 Dihedral : 26.357 179.209 7960 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 7.07 % Allowed : 21.21 % Favored : 71.72 % 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: -0.88 (0.77), residues: 114 helix: 0.43 (0.70), residues: 47 sheet: -0.58 (0.90), residues: 29 loop : -1.75 (1.09), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 6 TYR 0.016 0.004 TYR B 5 PHE 0.016 0.003 PHE B 68 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.65 (12970) covalent geometry : angle 1.08775 / 0.54 (20012) hydrogen bonds : bond 0.13256 / 15.03 ( 474) hydrogen bonds : angle 2.83563 / 3.58 ( 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.157 Fit side-chains REVERT: B 6 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.7931 (mtp180) REVERT: B 18 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8644 (mm-40) REVERT: B 26 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8633 (ttm-80) REVERT: B 35 ARG cc_start: 0.8525 (mmt90) cc_final: 0.8211 (mmt180) REVERT: B 96 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7890 (pt0) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.9058 time to fit residues: 21.0211 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 34 ASP 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: 0.9980 chunk 37 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 50.0000 chunk 55 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.077013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045939 restraints weight = 49764.083| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.29 r_work: 0.2797 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12970 Z= 0.457 Angle : 0.823 7.961 20012 Z= 0.433 Chirality : 0.057 0.382 2636 Planarity : 0.006 0.026 664 Dihedral : 26.304 176.484 7960 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 8.08 % Allowed : 20.20 % Favored : 71.72 % 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: -0.51 (0.77), residues: 114 helix: 0.88 (0.73), residues: 47 sheet: -0.58 (0.88), residues: 29 loop : -1.61 (1.05), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.011 0.002 TYR B 31 PHE 0.014 0.003 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.46 (12970) covalent geometry : angle 0.82265 / 0.43 (20012) hydrogen bonds : bond 0.10230 / 11.52 ( 474) hydrogen bonds : angle 2.67304 / 3.40 ( 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 : 0.117 Fit side-chains REVERT: B 6 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: B 12 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: B 35 ARG cc_start: 0.8544 (mmt90) cc_final: 0.8201 (mmt180) REVERT: B 96 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7927 (pt0) outliers start: 8 outliers final: 4 residues processed: 23 average time/residue: 0.8865 time to fit residues: 21.4753 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 : 0.095 ------------------------------------------------------------------------------- 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 99 LYS 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: 8.9990 chunk 53 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.076092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045171 restraints weight = 50087.169| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.00 r_work: 0.2768 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.102 12970 Z= 0.748 Angle : 1.161 10.776 20012 Z= 0.564 Chirality : 0.080 0.403 2636 Planarity : 0.008 0.042 664 Dihedral : 26.298 179.562 7960 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.06 % Allowed : 26.26 % 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: -0.99 (0.78), residues: 114 helix: 0.35 (0.70), residues: 47 sheet: -0.59 (0.91), residues: 29 loop : -1.87 (1.09), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 65 TYR 0.012 0.003 TYR B 5 PHE 0.011 0.003 PHE B 68 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01160 / 0.75 (12970) covalent geometry : angle 1.16077 / 0.56 (20012) hydrogen bonds : bond 0.13849 / 15.66 ( 474) hydrogen bonds : angle 2.92146 / 3.68 ( 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.174 Fit side-chains REVERT: B 6 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8092 (mtp180) outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.8865 time to fit residues: 20.5796 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG 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 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: 0.7980 chunk 8 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 overall best weight: 2.1382 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.078618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048237 restraints weight = 49178.979| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.70 r_work: 0.2947 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12970 Z= 0.228 Angle : 0.614 7.484 20012 Z= 0.358 Chirality : 0.041 0.369 2636 Planarity : 0.006 0.047 664 Dihedral : 26.283 174.779 7960 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.03 % Allowed : 29.29 % 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: -0.28 (0.79), residues: 114 helix: 1.55 (0.78), residues: 47 sheet: -1.12 (0.84), residues: 31 loop : -1.58 (1.01), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 26 TYR 0.017 0.002 TYR B 31 PHE 0.013 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.23 (12970) covalent geometry : angle 0.61365 / 0.36 (20012) hydrogen bonds : bond 0.07996 / 8.99 ( 474) hydrogen bonds : angle 2.54567 / 3.25 ( 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.136 Fit side-chains REVERT: B 6 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8200 (mtp180) REVERT: B 12 GLU cc_start: 0.8986 (mp0) cc_final: 0.8602 (mt-10) REVERT: B 35 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8330 (mmt180) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.7975 time to fit residues: 18.6070 Evaluate side-chains 23 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.076506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045672 restraints weight = 49778.517| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.82 r_work: 0.2801 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.094 12970 Z= 0.690 Angle : 1.095 9.960 20012 Z= 0.534 Chirality : 0.076 0.397 2636 Planarity : 0.008 0.043 664 Dihedral : 26.173 178.244 7960 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.03 % Allowed : 29.29 % 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: -0.75 (0.79), residues: 114 helix: 0.66 (0.73), residues: 47 sheet: -0.71 (0.88), residues: 29 loop : -1.68 (1.12), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 35 TYR 0.013 0.002 TYR B 40 PHE 0.011 0.003 PHE B 28 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.69 (12970) covalent geometry : angle 1.09469 / 0.53 (20012) hydrogen bonds : bond 0.12686 / 14.23 ( 474) hydrogen bonds : angle 2.83427 / 3.55 ( 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 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.183 Fit side-chains REVERT: B 6 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8175 (mtp180) REVERT: B 12 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: B 35 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8368 (mmt180) outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 0.8870 time to fit residues: 17.7952 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.078460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048044 restraints weight = 49590.997| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 0.76 r_work: 0.2930 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.4326 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= 0.224 Angle : 0.620 7.795 20012 Z= 0.357 Chirality : 0.042 0.372 2636 Planarity : 0.006 0.039 664 Dihedral : 26.191 174.797 7960 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.03 % Allowed : 29.29 % 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: -0.12 (0.80), residues: 114 helix: 1.63 (0.79), residues: 47 sheet: -1.23 (0.82), residues: 31 loop : -1.18 (1.06), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 26 TYR 0.015 0.002 TYR B 31 PHE 0.013 0.002 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.22 (12970) covalent geometry : angle 0.61962 / 0.36 (20012) hydrogen bonds : bond 0.08045 / 9.01 ( 474) hydrogen bonds : angle 2.52705 / 3.21 ( 857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.80 seconds wall clock time: 73 minutes 4.34 seconds (4384.34 seconds total)