Starting phenix.real_space_refine on Fri Jul 3 05:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.cif Found real_map, /net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.map" model { file = "/net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9owy_70948/07_2026/9owy_70948.cif" } resolution = 2.69 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 525 5.49 5 S 3 5.16 5 C 5626 2.51 5 N 2231 2.21 5 O 3817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12231 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': 26, 'rna2p_pyr': 15, 'rna3p_pur': 217, 'rna3p_pyr': 159} Link IDs: {'rna2p': 41, 'rna3p': 375} 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: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2293 Classifications: {'RNA': 108} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 41, 'rna3p_pyr': 50} Link IDs: {'rna2p': 16, 'rna3p': 91} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 0 Ad-hoc single atom residues: {' CA': 27} Chain breaks: 27 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 2.48, per 1000 atoms: 0.20 Number of scatterers: 12231 At special positions: 0 Unit cell: (120.269, 159.667, 128.563, 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 525 15.00 O 3817 8.00 N 2231 7.00 C 5626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 190.4 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 44.0% alpha, 16.4% beta 184 base pairs and 308 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... 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: 3.526A 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: 7.369A 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: 7.640A pdb=" N ALA B 85 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER B 46 " --> pdb=" O ALA B 85 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 467 hydrogen bonds 772 hydrogen bond angles 0 basepair planarities 184 basepair parallelities 308 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1131 1.32 - 1.44: 6478 1.44 - 1.56: 4895 1.56 - 1.68: 1049 1.68 - 1.80: 5 Bond restraints: 13558 Sorted by residual: bond pdb=" CA SER B 100 " pdb=" CB SER B 100 " ideal model delta sigma weight residual 1.529 1.422 0.107 1.55e-02 4.16e+03 4.73e+01 bond pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.37e-02 5.33e+03 2.19e+01 bond pdb=" CA ALA B 95 " pdb=" CB ALA B 95 " ideal model delta sigma weight residual 1.532 1.460 0.072 1.65e-02 3.67e+03 1.88e+01 bond pdb=" N9 A A 45 " pdb=" C4 A A 45 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.20e+01 bond pdb=" C SER B 100 " pdb=" O SER B 100 " ideal model delta sigma weight residual 1.236 1.204 0.033 1.15e-02 7.56e+03 8.06e+00 ... (remaining 13553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18447 2.36 - 4.72: 1714 4.72 - 7.08: 712 7.08 - 9.45: 51 9.45 - 11.81: 4 Bond angle restraints: 20928 Sorted by residual: angle pdb=" O3' C A 92 " pdb=" P C A 93 " pdb=" O5' C A 93 " ideal model delta sigma weight residual 104.00 94.29 9.71 1.50e+00 4.44e-01 4.19e+01 angle pdb=" O3' G A 200 " pdb=" P A A 201 " pdb=" O5' A A 201 " ideal model delta sigma weight residual 104.00 95.76 8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" O3' A A 50 " pdb=" P G A 51 " pdb=" O5' G A 51 " ideal model delta sigma weight residual 104.00 95.85 8.15 1.50e+00 4.44e-01 2.95e+01 angle pdb=" O2' C C 47 " pdb=" C2' C C 47 " pdb=" C1' C C 47 " ideal model delta sigma weight residual 111.80 103.65 8.15 1.50e+00 4.44e-01 2.95e+01 angle pdb=" O3' U A 191 " pdb=" P G A 192 " pdb=" O5' G A 192 " ideal model delta sigma weight residual 104.00 95.86 8.14 1.50e+00 4.44e-01 2.95e+01 ... (remaining 20923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 7157 35.87 - 71.75: 1480 71.75 - 107.62: 185 107.62 - 143.50: 9 143.50 - 179.37: 8 Dihedral angle restraints: 8839 sinusoidal: 8502 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual -160.00 9.40 -169.40 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U C 59 " pdb=" C1' U C 59 " pdb=" N1 U C 59 " pdb=" C2 U C 59 " ideal model delta sinusoidal sigma weight residual -128.00 51.37 -179.37 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C C -4 " pdb=" C1' C C -4 " pdb=" N1 C C -4 " pdb=" C2 C C -4 " ideal model delta sinusoidal sigma weight residual 232.00 54.43 177.57 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 8836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1925 0.125 - 0.249: 457 0.249 - 0.374: 150 0.374 - 0.498: 213 0.498 - 0.623: 16 Chirality restraints: 2761 Sorted by residual: chirality pdb=" P G A 268 " pdb=" OP1 G A 268 " pdb=" OP2 G A 268 " pdb=" O5' G A 268 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.70e+00 chirality pdb=" P C A 123 " pdb=" OP1 C A 123 " pdb=" OP2 C A 123 " pdb=" O5' C A 123 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" P G A 127 " pdb=" OP1 G A 127 " pdb=" OP2 G A 127 " pdb=" O5' G A 127 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.32e+00 ... (remaining 2758 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.412 9.50e-02 1.11e+02 1.85e-01 2.10e+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=" CA GLY B 110 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C GLY B 110 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY B 110 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU B 111 " 0.023 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 " -0.010 2.00e-02 2.50e+03 pdb=" N7 G A 299 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 299 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 299 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G A 299 " 0.006 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 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 5 1.81 - 2.58: 213 2.58 - 3.35: 14572 3.35 - 4.13: 47795 4.13 - 4.90: 58483 Nonbonded interactions: 121068 Sorted by model distance: nonbonded pdb=" OP2 U A 293 " pdb="CA CA A 521 " model vdw 1.037 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 1.368 3.690 nonbonded pdb=" OP2 C A 196 " pdb="CA CA A 525 " model vdw 1.770 3.250 ... (remaining 121063 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: 4.380 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.440 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: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 0.107 13558 Z= 0.672 Angle : 1.637 11.808 20928 Z= 0.965 Chirality : 0.167 0.623 2761 Planarity : 0.009 0.185 689 Dihedral : 27.939 179.369 8623 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 1.75 % Allowed : 2.63 % Favored : 95.61 % Rotamer: Outliers : 9.09 % Allowed : 24.24 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.79), residues: 114 helix: 1.16 (0.85), residues: 47 sheet: 0.87 (0.83), residues: 29 loop : -0.50 (0.96), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.006 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 0.00935 / 0.67 (13558) covalent geometry : angle 1.63691 / 0.96 (20928) hydrogen bonds : bond 0.21176 / 21.05 ( 512) hydrogen bonds : angle 10.09485 / 12.58 ( 901) *********************** 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: 9 poor density : 28 time to evaluate : 0.164 Fit side-chains REVERT: B 4 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9074 (tttp) REVERT: B 12 GLU cc_start: 0.8739 (mp0) cc_final: 0.8314 (mt-10) REVERT: B 112 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7151 (mppt) outliers start: 9 outliers final: 0 residues processed: 34 average time/residue: 0.8133 time to fit residues: 29.4743 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 : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 112 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.100086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.062843 restraints weight = 38500.168| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.60 r_work: 0.3141 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 13558 Z= 0.492 Angle : 0.759 10.774 20928 Z= 0.450 Chirality : 0.056 0.260 2761 Planarity : 0.007 0.037 689 Dihedral : 27.092 177.129 8376 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 10.10 % Allowed : 19.19 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.76), residues: 114 helix: 0.74 (0.70), residues: 48 sheet: 0.92 (0.85), residues: 29 loop : 0.09 (1.13), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.011 0.003 TYR B 94 PHE 0.020 0.004 PHE B 68 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.49 (13558) covalent geometry : angle 0.75854 / 0.45 (20928) hydrogen bonds : bond 0.13054 / 12.09 ( 512) hydrogen bonds : angle 2.94338 / 3.64 ( 901) *********************** 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 30 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.171 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 24 average time/residue: 0.8602 time to fit residues: 21.9971 Evaluate side-chains 22 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.100089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.060599 restraints weight = 41353.824| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.57 r_work: 0.3094 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 13558 Z= 0.464 Angle : 0.671 9.588 20928 Z= 0.405 Chirality : 0.049 0.255 2761 Planarity : 0.007 0.029 689 Dihedral : 26.824 174.595 8368 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 8.08 % Allowed : 19.19 % Favored : 72.73 % 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: 0.48 (0.78), residues: 114 helix: 0.41 (0.72), residues: 48 sheet: 0.03 (0.68), residues: 29 loop : 0.81 (1.28), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.020 0.004 TYR B 94 PHE 0.019 0.004 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.46 (13558) covalent geometry : angle 0.67092 / 0.41 (20928) hydrogen bonds : bond 0.11586 / 11.20 ( 512) hydrogen bonds : angle 2.89026 / 3.46 ( 901) *********************** 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 27 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.183 Fit side-chains REVERT: B 86 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8833 (mtp85) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.9517 time to fit residues: 25.1990 Evaluate side-chains 21 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 106 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.100773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061487 restraints weight = 40955.013| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.20 r_work: 0.3113 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13558 Z= 0.314 Angle : 0.563 9.712 20928 Z= 0.351 Chirality : 0.042 0.214 2761 Planarity : 0.005 0.022 689 Dihedral : 26.706 173.164 8368 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.02 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: 0.71 (0.81), residues: 114 helix: 0.70 (0.75), residues: 48 sheet: 0.11 (0.72), residues: 29 loop : 0.79 (1.31), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 86 TYR 0.008 0.002 TYR B 94 PHE 0.014 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.31 (13558) covalent geometry : angle 0.56318 / 0.35 (20928) hydrogen bonds : bond 0.09400 / 8.98 ( 512) hydrogen bonds : angle 2.49730 / 2.96 ( 901) *********************** 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 28 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.159 Fit side-chains REVERT: B 19 GLN cc_start: 0.9009 (mp10) cc_final: 0.8593 (mt0) outliers start: 8 outliers final: 1 residues processed: 26 average time/residue: 0.8319 time to fit residues: 22.9410 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.098105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059676 restraints weight = 37524.106| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.62 r_work: 0.3111 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 13558 Z= 0.542 Angle : 0.710 9.352 20928 Z= 0.427 Chirality : 0.055 0.260 2761 Planarity : 0.007 0.042 689 Dihedral : 26.697 174.725 8368 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 7.07 % Allowed : 25.25 % 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: 0.33 (0.80), residues: 114 helix: 0.15 (0.70), residues: 48 sheet: 0.13 (0.79), residues: 29 loop : 0.77 (1.30), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 59 TYR 0.008 0.002 TYR B 94 PHE 0.016 0.004 PHE B 68 HIS 0.002 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.54 (13558) covalent geometry : angle 0.71023 / 0.43 (20928) hydrogen bonds : bond 0.12831 / 12.30 ( 512) hydrogen bonds : angle 2.70929 / 3.19 ( 901) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.101 Fit side-chains REVERT: B 86 ARG cc_start: 0.9114 (mmm-85) cc_final: 0.8908 (mtp85) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.7796 time to fit residues: 18.3148 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 : 0.149 ------------------------------------------------------------------------------- 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 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 10 ASN B 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.061215 restraints weight = 37650.374| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.07 r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13558 Z= 0.298 Angle : 0.535 8.892 20928 Z= 0.336 Chirality : 0.040 0.215 2761 Planarity : 0.005 0.028 689 Dihedral : 26.641 173.629 8368 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.05 % Allowed : 25.25 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.82), residues: 114 helix: 0.84 (0.76), residues: 48 sheet: 0.38 (0.80), residues: 29 loop : 0.78 (1.30), residues: 37 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.011 0.002 TYR B 94 PHE 0.012 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.30 (13558) covalent geometry : angle 0.53459 / 0.34 (20928) hydrogen bonds : bond 0.09137 / 8.81 ( 512) hydrogen bonds : angle 2.45346 / 2.86 ( 901) *********************** 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 24 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.171 Fit side-chains REVERT: B 19 GLN cc_start: 0.8990 (mp10) cc_final: 0.8525 (mt0) REVERT: B 86 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8785 (mtp85) outliers start: 5 outliers final: 1 residues processed: 23 average time/residue: 0.9058 time to fit residues: 22.1647 Evaluate side-chains 20 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.099479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.061721 restraints weight = 37447.429| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.02 r_work: 0.3163 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13558 Z= 0.274 Angle : 0.510 7.900 20928 Z= 0.323 Chirality : 0.038 0.200 2761 Planarity : 0.005 0.022 689 Dihedral : 26.464 174.530 8368 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.05 % Allowed : 27.27 % 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: 1.22 (0.84), residues: 114 helix: 1.05 (0.79), residues: 47 sheet: 1.27 (0.81), residues: 26 loop : 0.39 (1.24), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 62 TYR 0.013 0.002 TYR B 94 PHE 0.006 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.27 (13558) covalent geometry : angle 0.51048 / 0.32 (20928) hydrogen bonds : bond 0.09050 / 8.80 ( 512) hydrogen bonds : angle 2.40992 / 2.81 ( 901) *********************** 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: 5 poor density : 21 time to evaluate : 0.164 Fit side-chains REVERT: B 19 GLN cc_start: 0.8986 (mp10) cc_final: 0.8520 (mt0) REVERT: B 86 ARG cc_start: 0.8988 (mmm-85) cc_final: 0.8777 (mtp85) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.7477 time to fit residues: 19.8760 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 32 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 overall best weight: 1.5380 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.100223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063027 restraints weight = 37487.072| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 0.77 r_work: 0.3191 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13558 Z= 0.208 Angle : 0.471 7.390 20928 Z= 0.302 Chirality : 0.035 0.185 2761 Planarity : 0.005 0.023 689 Dihedral : 26.399 174.591 8368 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.06 % Allowed : 24.24 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.85), residues: 114 helix: 1.21 (0.80), residues: 47 sheet: 1.28 (0.80), residues: 26 loop : 0.44 (1.25), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.011 0.002 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.21 (13558) covalent geometry : angle 0.47088 / 0.30 (20928) hydrogen bonds : bond 0.08297 / 8.08 ( 512) hydrogen bonds : angle 2.36455 / 2.74 ( 901) *********************** 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 26 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.171 Fit side-chains REVERT: B 19 GLN cc_start: 0.8964 (mp10) cc_final: 0.8511 (mt0) REVERT: B 83 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.8974 (mm) outliers start: 6 outliers final: 2 residues processed: 23 average time/residue: 0.8355 time to fit residues: 20.4980 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 : 0.144 ------------------------------------------------------------------------------- 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 83 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.097852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059779 restraints weight = 37265.862| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.60 r_work: 0.3092 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 13558 Z= 0.556 Angle : 0.694 6.612 20928 Z= 0.415 Chirality : 0.055 0.259 2761 Planarity : 0.007 0.036 689 Dihedral : 26.432 174.959 8368 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.07 % Allowed : 23.23 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.82), residues: 114 helix: 0.42 (0.75), residues: 47 sheet: 0.75 (0.77), residues: 26 loop : 0.09 (1.24), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 62 TYR 0.018 0.003 TYR B 94 PHE 0.017 0.004 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.56 (13558) covalent geometry : angle 0.69388 / 0.41 (20928) hydrogen bonds : bond 0.11959 / 11.54 ( 512) hydrogen bonds : angle 2.64328 / 3.02 ( 901) *********************** 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 25 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.111 Fit side-chains REVERT: B 19 GLN cc_start: 0.9039 (mp10) cc_final: 0.8569 (mt0) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.7431 time to fit residues: 17.4484 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 : 0.159 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.098347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.060425 restraints weight = 37663.094| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.42 r_work: 0.3119 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 13558 Z= 0.438 Angle : 0.610 6.009 20928 Z= 0.374 Chirality : 0.048 0.244 2761 Planarity : 0.006 0.024 689 Dihedral : 26.525 174.539 8368 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.04 % Allowed : 28.28 % 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: 0.65 (0.82), residues: 114 helix: 0.79 (0.77), residues: 47 sheet: 0.76 (0.79), residues: 26 loop : -0.05 (1.21), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 42 TYR 0.009 0.002 TYR B 94 PHE 0.015 0.003 PHE B 68 HIS 0.001 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.44 (13558) covalent geometry : angle 0.60955 / 0.37 (20928) hydrogen bonds : bond 0.10138 / 9.80 ( 512) hydrogen bonds : angle 2.57015 / 2.93 ( 901) ********************** 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: 4 poor density : 17 time to evaluate : 0.166 Fit side-chains REVERT: B 19 GLN cc_start: 0.9016 (mp10) cc_final: 0.8555 (mt0) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.8356 time to fit residues: 16.9091 Evaluate side-chains 19 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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: 62 random chunks: chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.098867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.061024 restraints weight = 37582.819| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.96 r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13558 Z= 0.283 Angle : 0.526 7.010 20928 Z= 0.331 Chirality : 0.039 0.216 2761 Planarity : 0.005 0.023 689 Dihedral : 26.497 173.827 8368 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.03 % Allowed : 30.30 % 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: 0.96 (0.85), residues: 114 helix: 1.09 (0.81), residues: 47 sheet: 0.89 (0.78), residues: 26 loop : 0.10 (1.24), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.010 0.002 TYR B 94 PHE 0.009 0.002 PHE B 68 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.28 (13558) covalent geometry : angle 0.52587 / 0.33 (20928) hydrogen bonds : bond 0.09202 / 8.90 ( 512) hydrogen bonds : angle 2.50138 / 2.89 ( 901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5465.16 seconds wall clock time: 93 minutes 41.00 seconds (5621.00 seconds total)