Starting phenix.real_space_refine on Fri Jul 3 04:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944.map" model { file = "/net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owu_70944/07_2026/9owu_70944_neut.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 25 9.91 5 P 515 5.49 5 S 3 5.16 5 C 5530 2.51 5 N 2189 2.21 5 O 3749 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: 12011 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 15, 'rna3p_pur': 220, 'rna3p_pyr': 159} Link IDs: {'rna2p': 38, 'rna3p': 378} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1889 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 33, 'rna3p_pyr': 40} Link IDs: {'rna2p': 15, 'rna3p': 73} Chain: "E" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 188 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 0 Ad-hoc single atom residues: {' CA': 25} Chain breaks: 25 Time building chain proxies: 2.81, per 1000 atoms: 0.23 Number of scatterers: 12011 At special positions: 0 Unit cell: (125.453, 145.152, 163.814, 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 25 19.99 S 3 16.00 P 515 15.00 O 3749 8.00 N 2189 7.00 C 5530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 164.9 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 1 sheets defined 52.6% alpha, 16.4% beta 176 base pairs and 311 stacking pairs defined. Time for finding SS restraints: 2.16 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 48 through 52 Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 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: 6.090A 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: 6.192A pdb=" N GLY B 44 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 448 hydrogen bonds 766 hydrogen bond angles 0 basepair planarities 176 basepair parallelities 311 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 1.31 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: 1132 1.32 - 1.44: 6365 1.44 - 1.56: 4786 1.56 - 1.68: 1027 1.68 - 1.80: 5 Bond restraints: 13315 Sorted by residual: bond pdb=" CA SER B 48 " pdb=" CB SER B 48 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.55e-02 4.16e+03 1.66e+01 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 1.07e+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 9.50e+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 7.70e+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 7.17e+00 ... (remaining 13310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 18176 2.39 - 4.77: 1629 4.77 - 7.16: 699 7.16 - 9.55: 38 9.55 - 11.94: 4 Bond angle restraints: 20546 Sorted by residual: angle pdb=" O3' U A 75 " pdb=" C3' U A 75 " pdb=" C2' U A 75 " ideal model delta sigma weight residual 109.50 119.35 -9.85 1.50e+00 4.44e-01 4.32e+01 angle pdb=" O3' G A 230 " pdb=" P A A 231 " pdb=" O5' A A 231 " ideal model delta sigma weight residual 104.00 112.90 -8.90 1.50e+00 4.44e-01 3.52e+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 96.75 5.85 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C4' C C 69 " pdb=" C3' C C 69 " pdb=" C2' C C 69 " ideal model delta sigma weight residual 102.60 96.93 5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" O3' C C 69 " pdb=" P G C 70 " pdb=" O5' G C 70 " ideal model delta sigma weight residual 104.00 95.57 8.43 1.50e+00 4.44e-01 3.16e+01 ... (remaining 20541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 7031 35.94 - 71.88: 1452 71.88 - 107.81: 179 107.81 - 143.75: 5 143.75 - 179.69: 9 Dihedral angle restraints: 8676 sinusoidal: 8339 harmonic: 337 Sorted by residual: dihedral pdb=" C4' U A 75 " pdb=" C3' U A 75 " pdb=" C2' U A 75 " pdb=" C1' U A 75 " ideal model delta sinusoidal sigma weight residual -35.00 31.01 -66.01 1 8.00e+00 1.56e-02 8.90e+01 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 10.35 -170.35 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" C5' U A 75 " pdb=" C4' U A 75 " pdb=" C3' U A 75 " pdb=" O3' U A 75 " ideal model delta sinusoidal sigma weight residual 147.00 83.94 63.06 1 8.00e+00 1.56e-02 8.20e+01 ... (remaining 8673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1840 0.113 - 0.225: 486 0.225 - 0.338: 64 0.338 - 0.451: 245 0.451 - 0.563: 76 Chirality restraints: 2711 Sorted by residual: chirality pdb=" P C C -6 " pdb=" OP1 C C -6 " pdb=" OP2 C C -6 " pdb=" O5' C C -6 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P C A 367 " pdb=" OP1 C A 367 " pdb=" OP2 C A 367 " pdb=" O5' C A 367 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.92e+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 7.88e+00 ... (remaining 2708 not shown) Planarity restraints: 679 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 " 0.003 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 2.06e-02 1.27e+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 " -0.018 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 " 0.003 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 1.64e-02 6.04e+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 676 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 4 1.81 - 2.58: 182 2.58 - 3.36: 14555 3.36 - 4.13: 46378 4.13 - 4.90: 57069 Nonbonded interactions: 118188 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 522 " model vdw 1.038 3.250 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 1.367 3.690 nonbonded pdb=" OP2 A A 364 " pdb=" N9 G A 365 " model vdw 1.835 3.120 ... (remaining 118183 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.130 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 0.063 13315 Z= 0.651 Angle : 1.621 11.936 20546 Z= 0.956 Chirality : 0.171 0.563 2711 Planarity : 0.008 0.186 679 Dihedral : 27.830 179.688 8460 Min Nonbonded Distance : 1.038 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.89 (0.81), residues: 114 helix: 1.32 (0.86), residues: 46 sheet: 0.92 (0.81), residues: 29 loop : -0.46 (1.06), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.010 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 0.00922 / 0.65 (13315) covalent geometry : angle 1.62141 / 0.96 (20546) hydrogen bonds : bond 0.20596 / 19.51 ( 497) hydrogen bonds : angle 9.27334 / 11.22 ( 895) *********************** 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 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.115 Fit side-chains REVERT: B 12 GLU cc_start: 0.8489 (mp0) cc_final: 0.7681 (mp0) REVERT: B 46 SER cc_start: 0.9060 (m) cc_final: 0.8757 (p) REVERT: B 63 TYR cc_start: 0.9128 (m-10) cc_final: 0.8855 (m-10) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 0.6645 time to fit residues: 27.6945 Evaluate side-chains 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 97 VAL 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: 6.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 10.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.090810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058488 restraints weight = 54719.195| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.61 r_work: 0.2877 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 13315 Z= 0.565 Angle : 0.862 9.525 20546 Z= 0.506 Chirality : 0.057 0.423 2711 Planarity : 0.007 0.044 679 Dihedral : 27.033 178.889 8208 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 9.09 % Allowed : 27.27 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.73), residues: 114 helix: 1.07 (0.69), residues: 48 sheet: 0.51 (0.70), residues: 29 loop : -0.25 (1.12), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 59 TYR 0.010 0.003 TYR B 31 PHE 0.009 0.002 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.56 (13315) covalent geometry : angle 0.86213 / 0.51 (20546) hydrogen bonds : bond 0.13180 / 13.82 ( 497) hydrogen bonds : angle 3.12409 / 3.47 ( 895) *********************** 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 29 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.160 Fit side-chains REVERT: B 6 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8719 (mtm180) REVERT: B 12 GLU cc_start: 0.8582 (mp0) cc_final: 0.7980 (mp0) REVERT: B 15 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7727 (mt-10) REVERT: B 46 SER cc_start: 0.9221 (m) cc_final: 0.8526 (p) REVERT: B 111 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8380 (tm) outliers start: 9 outliers final: 4 residues processed: 26 average time/residue: 0.6652 time to fit residues: 18.7089 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 : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 37 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.091571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056304 restraints weight = 53765.134| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.15 r_work: 0.2915 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13315 Z= 0.307 Angle : 0.573 8.582 20546 Z= 0.358 Chirality : 0.040 0.365 2711 Planarity : 0.005 0.020 679 Dihedral : 26.933 174.401 8207 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 28.28 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.78), residues: 114 helix: 1.65 (0.73), residues: 48 sheet: 0.51 (0.77), residues: 29 loop : -0.03 (1.18), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 86 TYR 0.008 0.002 TYR B 5 PHE 0.006 0.002 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.31 (13315) covalent geometry : angle 0.57318 / 0.36 (20546) hydrogen bonds : bond 0.08869 / 8.53 ( 497) hydrogen bonds : angle 2.65757 / 3.03 ( 895) *********************** 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: 6 poor density : 24 time to evaluate : 0.097 Fit side-chains REVERT: B 12 GLU cc_start: 0.8577 (mp0) cc_final: 0.7418 (mp0) REVERT: B 15 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 32 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8421 (p) REVERT: B 46 SER cc_start: 0.9205 (m) cc_final: 0.8404 (p) REVERT: B 111 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8566 (tm) outliers start: 6 outliers final: 1 residues processed: 27 average time/residue: 0.6911 time to fit residues: 19.9013 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 : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.090619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.056335 restraints weight = 54388.988| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.05 r_work: 0.2930 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13315 Z= 0.389 Angle : 0.620 9.720 20546 Z= 0.382 Chirality : 0.043 0.310 2711 Planarity : 0.006 0.046 679 Dihedral : 26.728 175.038 8207 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 35.35 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.78), residues: 114 helix: 0.92 (0.72), residues: 48 sheet: -0.04 (0.72), residues: 29 loop : 0.26 (1.25), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 59 TYR 0.008 0.002 TYR B 5 PHE 0.005 0.002 PHE B 28 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.39 (13315) covalent geometry : angle 0.61985 / 0.38 (20546) hydrogen bonds : bond 0.09545 / 9.25 ( 497) hydrogen bonds : angle 2.60660 / 2.97 ( 895) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.132 Fit side-chains REVERT: B 12 GLU cc_start: 0.8568 (mp0) cc_final: 0.7499 (mp0) REVERT: B 15 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 32 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 46 SER cc_start: 0.9197 (m) cc_final: 0.8437 (p) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.6539 time to fit residues: 17.5494 Evaluate side-chains 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 0.0020 chunk 57 optimal weight: 50.0000 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.090491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057784 restraints weight = 55867.551| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.45 r_work: 0.2939 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 13315 Z= 0.367 Angle : 0.593 10.121 20546 Z= 0.366 Chirality : 0.042 0.315 2711 Planarity : 0.005 0.039 679 Dihedral : 26.659 175.372 8207 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 36.36 % Favored : 57.58 % 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: 0.31 (0.77), residues: 114 helix: 0.94 (0.75), residues: 48 sheet: -0.29 (0.67), residues: 29 loop : -0.11 (1.19), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 59 TYR 0.010 0.002 TYR B 5 PHE 0.006 0.002 PHE B 28 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.37 (13315) covalent geometry : angle 0.59308 / 0.37 (20546) hydrogen bonds : bond 0.08723 / 8.48 ( 497) hydrogen bonds : angle 2.54218 / 2.88 ( 895) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.189 Fit side-chains REVERT: B 12 GLU cc_start: 0.8558 (mp0) cc_final: 0.7505 (mp0) REVERT: B 15 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 26 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8313 (ttp80) REVERT: B 32 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8421 (p) REVERT: B 46 SER cc_start: 0.9165 (m) cc_final: 0.8429 (p) outliers start: 6 outliers final: 1 residues processed: 25 average time/residue: 0.6728 time to fit residues: 17.9862 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.089938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057221 restraints weight = 55857.632| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.91 r_work: 0.2919 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13315 Z= 0.449 Angle : 0.654 13.525 20546 Z= 0.396 Chirality : 0.046 0.311 2711 Planarity : 0.006 0.039 679 Dihedral : 26.626 175.888 8205 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 7.07 % Allowed : 35.35 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.76), residues: 114 helix: 0.79 (0.75), residues: 48 sheet: -0.49 (0.66), residues: 29 loop : -0.24 (1.17), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 59 TYR 0.010 0.002 TYR B 5 PHE 0.008 0.002 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.45 (13315) covalent geometry : angle 0.65428 / 0.40 (20546) hydrogen bonds : bond 0.09942 / 9.70 ( 497) hydrogen bonds : angle 2.61998 / 2.94 ( 895) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.165 Fit side-chains REVERT: B 15 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 32 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8438 (p) REVERT: B 46 SER cc_start: 0.9187 (m) cc_final: 0.8440 (p) outliers start: 7 outliers final: 1 residues processed: 25 average time/residue: 0.7043 time to fit residues: 18.7385 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.090342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057571 restraints weight = 55527.027| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.34 r_work: 0.2941 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13315 Z= 0.324 Angle : 0.570 12.103 20546 Z= 0.351 Chirality : 0.040 0.302 2711 Planarity : 0.005 0.037 679 Dihedral : 26.627 176.218 8205 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.04 % Allowed : 37.37 % Favored : 58.59 % 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: 0.17 (0.76), residues: 114 helix: 0.99 (0.75), residues: 48 sheet: -0.31 (0.67), residues: 29 loop : -0.51 (1.14), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 59 TYR 0.008 0.002 TYR B 31 PHE 0.008 0.002 PHE B 68 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.32 (13315) covalent geometry : angle 0.56977 / 0.35 (20546) hydrogen bonds : bond 0.08174 / 7.91 ( 497) hydrogen bonds : angle 2.46216 / 2.78 ( 895) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.097 Fit side-chains REVERT: B 12 GLU cc_start: 0.8558 (mp0) cc_final: 0.7531 (mp0) REVERT: B 15 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 32 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8372 (p) REVERT: B 46 SER cc_start: 0.9167 (m) cc_final: 0.8408 (p) outliers start: 4 outliers final: 0 residues processed: 25 average time/residue: 0.7014 time to fit residues: 18.7727 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.090228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058377 restraints weight = 54614.095| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.95 r_work: 0.2902 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13315 Z= 0.392 Angle : 0.620 11.328 20546 Z= 0.377 Chirality : 0.043 0.305 2711 Planarity : 0.005 0.040 679 Dihedral : 26.564 176.269 8205 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.05 % Allowed : 35.35 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.78), residues: 114 helix: 0.85 (0.77), residues: 48 sheet: -0.98 (0.71), residues: 31 loop : 0.02 (1.18), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 59 TYR 0.008 0.002 TYR B 31 PHE 0.011 0.002 PHE B 28 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.39 (13315) covalent geometry : angle 0.61992 / 0.38 (20546) hydrogen bonds : bond 0.09476 / 9.21 ( 497) hydrogen bonds : angle 2.58887 / 2.84 ( 895) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.124 Fit side-chains REVERT: B 15 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 32 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8420 (p) REVERT: B 46 SER cc_start: 0.9179 (m) cc_final: 0.8408 (p) outliers start: 5 outliers final: 1 residues processed: 23 average time/residue: 0.7280 time to fit residues: 17.9311 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 51 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.090325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.058649 restraints weight = 54230.935| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.66 r_work: 0.2929 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13315 Z= 0.352 Angle : 0.582 11.020 20546 Z= 0.357 Chirality : 0.041 0.301 2711 Planarity : 0.005 0.042 679 Dihedral : 26.531 176.594 8205 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.03 % Allowed : 37.37 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.79), residues: 114 helix: 1.00 (0.78), residues: 48 sheet: -0.98 (0.74), residues: 31 loop : -0.00 (1.18), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 59 TYR 0.009 0.002 TYR B 5 PHE 0.014 0.002 PHE B 28 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.35 (13315) covalent geometry : angle 0.58234 / 0.36 (20546) hydrogen bonds : bond 0.08351 / 8.13 ( 497) hydrogen bonds : angle 2.51969 / 2.80 ( 895) *********************** 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 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 Fit side-chains REVERT: B 12 GLU cc_start: 0.8586 (mp0) cc_final: 0.7575 (mp0) REVERT: B 15 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7711 (mt-10) REVERT: B 32 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 46 SER cc_start: 0.9172 (m) cc_final: 0.8404 (p) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 0.7882 time to fit residues: 18.4855 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.059225 restraints weight = 55049.936| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.08 r_work: 0.2945 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13315 Z= 0.230 Angle : 0.518 11.849 20546 Z= 0.322 Chirality : 0.036 0.287 2711 Planarity : 0.005 0.027 679 Dihedral : 26.470 176.342 8205 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.03 % Allowed : 38.38 % Favored : 58.59 % 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 (0.80), residues: 114 helix: 1.19 (0.79), residues: 48 sheet: -0.60 (0.76), residues: 28 loop : -0.18 (1.14), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 59 TYR 0.008 0.001 TYR B 31 PHE 0.009 0.002 PHE B 28 HIS 0.001 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.23 (13315) covalent geometry : angle 0.51764 / 0.32 (20546) hydrogen bonds : bond 0.07647 / 7.43 ( 497) hydrogen bonds : angle 2.45179 / 2.71 ( 895) ********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.193 Fit side-chains REVERT: B 12 GLU cc_start: 0.8555 (mp0) cc_final: 0.7564 (mp0) REVERT: B 15 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 32 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 46 SER cc_start: 0.9170 (m) cc_final: 0.8377 (p) outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 0.7671 time to fit residues: 18.6624 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.089258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056015 restraints weight = 54622.966| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.99 r_work: 0.2879 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.085 13315 Z= 0.624 Angle : 0.778 10.112 20546 Z= 0.459 Chirality : 0.055 0.320 2711 Planarity : 0.006 0.036 679 Dihedral : 26.479 175.356 8205 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.04 % Allowed : 38.38 % Favored : 57.58 % 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: -0.43 (0.76), residues: 114 helix: 0.64 (0.76), residues: 48 sheet: -1.06 (0.68), residues: 29 loop : -0.60 (1.12), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 59 TYR 0.011 0.002 TYR B 31 PHE 0.011 0.003 PHE B 28 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.01019 / 0.62 (13315) covalent geometry : angle 0.77830 / 0.46 (20546) hydrogen bonds : bond 0.11593 / 11.41 ( 497) hydrogen bonds : angle 2.80161 / 3.04 ( 895) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4487.87 seconds wall clock time: 77 minutes 8.59 seconds (4628.59 seconds total)