Starting phenix.real_space_refine on Thu Jul 2 01:53:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2s_43757/07_2026/8w2s_43757.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 137 5.49 5 S 11 5.16 5 C 3025 2.51 5 N 1051 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5688 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2761 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 332} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2927 Classifications: {'RNA': 137} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 55} Link IDs: {'rna2p': 13, 'rna3p': 123} Time building chain proxies: 1.53, per 1000 atoms: 0.27 Number of scatterers: 5688 At special positions: 0 Unit cell: (86.6528, 86.6528, 115.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 137 15.00 O 1464 8.00 N 1051 7.00 C 3025 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: 0.47 Conformation dependent library (CDL) restraints added in 108.6 milliseconds 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 56.0% alpha, 5.3% beta 50 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 75 removed outlier: 3.690A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.836A pdb=" N GLU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.665A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'A' and resid 212 through 225 removed outlier: 3.521A pdb=" N ASP A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.518A pdb=" N ARG A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.617A pdb=" N ILE A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 removed outlier: 4.166A pdb=" N GLU A 580 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASP A 581 " --> pdb=" O GLY A 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 583 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 608 through 614 Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'A' and resid 640 through 643 removed outlier: 3.569A pdb=" N ILE A 641 " --> pdb=" O PHE A 648 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1109 1.33 - 1.45: 2107 1.45 - 1.57: 2567 1.57 - 1.69: 273 1.69 - 1.81: 16 Bond restraints: 6072 Sorted by residual: bond pdb=" N9 A B 118 " pdb=" C4 A B 118 " ideal model delta sigma weight residual 1.374 1.385 -0.011 6.00e-03 2.78e+04 3.13e+00 bond pdb=" N1 C B 126 " pdb=" C2 C B 126 " ideal model delta sigma weight residual 1.397 1.413 -0.016 1.00e-02 1.00e+04 2.68e+00 bond pdb=" CB GLU A 107 " pdb=" CG GLU A 107 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" C3' U B 92 " pdb=" O3' U B 92 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.51e+00 bond pdb=" C8 G B 143 " pdb=" N7 G B 143 " ideal model delta sigma weight residual 1.305 1.296 0.009 6.00e-03 2.78e+04 2.50e+00 ... (remaining 6067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 8670 2.69 - 5.37: 130 5.37 - 8.06: 27 8.06 - 10.74: 6 10.74 - 13.43: 4 Bond angle restraints: 8837 Sorted by residual: angle pdb=" N LYS A 172 " pdb=" CA LYS A 172 " pdb=" C LYS A 172 " ideal model delta sigma weight residual 108.67 95.45 13.22 1.55e+00 4.16e-01 7.27e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 111.33 120.20 -8.87 1.21e+00 6.83e-01 5.38e+01 angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 124.83 -10.83 1.50e+00 4.44e-01 5.21e+01 angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 117.21 -9.01 1.50e+00 4.44e-01 3.61e+01 angle pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" C THR A 261 " ideal model delta sigma weight residual 108.63 99.71 8.92 1.60e+00 3.91e-01 3.10e+01 ... (remaining 8832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 3552 35.33 - 70.66: 282 70.66 - 105.99: 33 105.99 - 141.32: 1 141.32 - 176.65: 2 Dihedral angle restraints: 3870 sinusoidal: 2874 harmonic: 996 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 48.65 -176.65 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS A 181 " pdb=" C LYS A 181 " pdb=" N CYS A 182 " pdb=" CA CYS A 182 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual 254.00 176.43 77.57 1 1.70e+01 3.46e-03 2.61e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 1085 0.175 - 0.350: 3 0.350 - 0.524: 0 0.524 - 0.699: 0 0.699 - 0.874: 1 Chirality restraints: 1089 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' G B 122 " pdb=" C4' G B 122 " pdb=" O3' G B 122 " pdb=" C2' G B 122 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1086 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " 0.066 2.00e-02 2.50e+03 3.07e-02 2.82e+01 pdb=" N9 G B 142 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 142 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 142 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G B 142 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 142 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G B 142 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 137 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ARG A 137 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 137 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 138 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 173 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ARG A 173 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG A 173 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 174 " -0.011 2.00e-02 2.50e+03 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1441 2.81 - 3.33: 5025 3.33 - 3.86: 11190 3.86 - 4.38: 12754 4.38 - 4.90: 17411 Nonbonded interactions: 47821 Sorted by model distance: nonbonded pdb=" O2' G B 11 " pdb=" O4' A B 12 " model vdw 2.289 3.040 nonbonded pdb=" OP2 U B 91 " pdb=" O2' U B 92 " model vdw 2.296 3.040 nonbonded pdb=" O PRO A 558 " pdb=" O2' U B 22 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU A 212 " pdb=" OG SER A 214 " model vdw 2.322 3.040 nonbonded pdb=" N2 G B 117 " pdb=" OP2 A B 120 " model vdw 2.340 3.120 ... (remaining 47816 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: 2.240 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.390 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6072 Z= 0.256 Angle : 0.890 13.428 8837 Z= 0.649 Chirality : 0.049 0.874 1089 Planarity : 0.005 0.048 621 Dihedral : 20.847 176.648 3218 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.44), residues: 331 helix: -0.51 (0.37), residues: 170 sheet: 1.34 (1.12), residues: 10 loop : -1.46 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.021 0.003 TYR A 97 PHE 0.016 0.002 PHE A 236 TRP 0.013 0.002 TRP A 127 HIS 0.008 0.002 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.26 ( 6072) covalent geometry : angle 0.88958 / 0.65 ( 8837) hydrogen bonds : bond 0.12798 / 9.62 ( 254) hydrogen bonds : angle 5.40498 / 3.95 ( 578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.149 Fit side-chains REVERT: A 124 LYS cc_start: 0.8091 (tppt) cc_final: 0.7772 (mtpt) REVERT: A 248 GLN cc_start: 0.9077 (mt0) cc_final: 0.8659 (mp10) REVERT: A 579 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7959 (mtpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1086 time to fit residues: 6.9695 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.151060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107206 restraints weight = 11872.661| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.09 r_work: 0.3438 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6072 Z= 0.146 Angle : 0.577 10.807 8837 Z= 0.342 Chirality : 0.042 0.720 1089 Planarity : 0.004 0.034 621 Dihedral : 21.765 166.620 2488 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.05 % Allowed : 12.29 % Favored : 85.67 % 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: -0.31 (0.46), residues: 331 helix: 0.61 (0.40), residues: 170 sheet: 1.01 (1.12), residues: 10 loop : -1.22 (0.52), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.018 0.002 TYR A 97 PHE 0.008 0.001 PHE A 570 TRP 0.009 0.002 TRP A 120 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 6072) covalent geometry : angle 0.57690 / 0.34 ( 8837) hydrogen bonds : bond 0.05898 / 3.96 ( 254) hydrogen bonds : angle 3.97842 / 2.91 ( 578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8169 (tppt) cc_final: 0.7787 (mtpt) REVERT: A 248 GLN cc_start: 0.9035 (mt0) cc_final: 0.8582 (mp10) REVERT: A 579 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8169 (mtpp) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.1067 time to fit residues: 6.6434 Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 10.9990 chunk 3 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.148238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103792 restraints weight = 11655.728| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.05 r_work: 0.3375 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6072 Z= 0.118 Angle : 0.510 10.137 8837 Z= 0.305 Chirality : 0.039 0.649 1089 Planarity : 0.004 0.028 621 Dihedral : 21.710 168.946 2488 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.73 % Allowed : 11.60 % Favored : 85.67 % 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: 0.22 (0.49), residues: 331 helix: 1.10 (0.41), residues: 174 sheet: 0.80 (1.12), residues: 10 loop : -1.07 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.013 0.002 TYR A 97 PHE 0.010 0.001 PHE A 570 TRP 0.007 0.001 TRP A 120 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 ( 6072) covalent geometry : angle 0.50968 / 0.31 ( 8837) hydrogen bonds : bond 0.04915 / 3.25 ( 254) hydrogen bonds : angle 3.66511 / 2.68 ( 578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9061 (mt0) cc_final: 0.8588 (mp10) REVERT: A 579 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8166 (mtpp) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.1070 time to fit residues: 6.7675 Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.146901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102449 restraints weight = 11676.748| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.07 r_work: 0.3347 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6072 Z= 0.132 Angle : 0.508 9.905 8837 Z= 0.304 Chirality : 0.040 0.643 1089 Planarity : 0.004 0.035 621 Dihedral : 21.626 167.434 2488 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.41 % Allowed : 12.63 % Favored : 83.96 % 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: 0.30 (0.49), residues: 331 helix: 1.20 (0.41), residues: 174 sheet: 0.87 (1.11), residues: 10 loop : -1.09 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.012 0.002 TYR A 97 PHE 0.009 0.001 PHE A 570 TRP 0.006 0.001 TRP A 120 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 6072) covalent geometry : angle 0.50805 / 0.30 ( 8837) hydrogen bonds : bond 0.05013 / 3.28 ( 254) hydrogen bonds : angle 3.63776 / 2.66 ( 578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9070 (mt0) cc_final: 0.8573 (mp10) REVERT: A 579 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8163 (mtpp) REVERT: A 607 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5354 (tt) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.0986 time to fit residues: 6.3968 Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 649 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.0060 chunk 39 optimal weight: 10.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 0.0470 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN A 645 ASN A 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.151209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107689 restraints weight = 11974.330| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.10 r_work: 0.3447 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6072 Z= 0.103 Angle : 0.483 9.463 8837 Z= 0.290 Chirality : 0.038 0.593 1089 Planarity : 0.003 0.035 621 Dihedral : 21.620 167.962 2488 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.73 % Allowed : 12.29 % Favored : 84.98 % 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: 0.50 (0.48), residues: 331 helix: 1.38 (0.41), residues: 174 sheet: 0.93 (1.13), residues: 10 loop : -1.02 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 152 TYR 0.010 0.002 TYR A 97 PHE 0.013 0.001 PHE A 236 TRP 0.005 0.001 TRP A 120 HIS 0.002 0.000 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 6072) covalent geometry : angle 0.48317 / 0.29 ( 8837) hydrogen bonds : bond 0.04508 / 2.98 ( 254) hydrogen bonds : angle 3.51556 / 2.56 ( 578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 248 GLN cc_start: 0.9037 (mt0) cc_final: 0.8547 (mp10) REVERT: A 579 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8126 (mtpp) REVERT: A 607 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5420 (tt) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0967 time to fit residues: 5.8625 Evaluate side-chains 44 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 11.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.147715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103613 restraints weight = 11805.001| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.15 r_work: 0.3380 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6072 Z= 0.180 Angle : 0.535 9.716 8837 Z= 0.316 Chirality : 0.041 0.646 1089 Planarity : 0.004 0.036 621 Dihedral : 21.508 167.446 2488 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.39 % Allowed : 12.97 % Favored : 84.64 % 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: 0.53 (0.49), residues: 331 helix: 1.48 (0.41), residues: 174 sheet: 0.80 (1.12), residues: 10 loop : -1.09 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 228 TYR 0.015 0.002 TYR A 76 PHE 0.011 0.002 PHE A 570 TRP 0.007 0.001 TRP A 120 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 ( 6072) covalent geometry : angle 0.53490 / 0.32 ( 8837) hydrogen bonds : bond 0.05386 / 3.49 ( 254) hydrogen bonds : angle 3.56173 / 2.61 ( 578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8446 (mmm160) REVERT: A 248 GLN cc_start: 0.9028 (mt0) cc_final: 0.8531 (mp10) REVERT: A 579 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8189 (mtpp) REVERT: A 607 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5454 (tt) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.0991 time to fit residues: 5.6327 Evaluate side-chains 46 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.097679 restraints weight = 11851.936| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.13 r_work: 0.3278 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6072 Z= 0.184 Angle : 0.564 10.307 8837 Z= 0.333 Chirality : 0.043 0.700 1089 Planarity : 0.004 0.043 621 Dihedral : 21.567 169.600 2488 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.41 % Allowed : 12.29 % Favored : 84.30 % 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: 0.41 (0.49), residues: 331 helix: 1.47 (0.40), residues: 174 sheet: 1.00 (1.16), residues: 10 loop : -1.29 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 173 TYR 0.020 0.003 TYR A 76 PHE 0.013 0.002 PHE A 83 TRP 0.009 0.001 TRP A 120 HIS 0.005 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 ( 6072) covalent geometry : angle 0.56436 / 0.33 ( 8837) hydrogen bonds : bond 0.05866 / 3.73 ( 254) hydrogen bonds : angle 3.62798 / 2.66 ( 578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8870 (mmm160) cc_final: 0.8424 (mmm160) REVERT: A 248 GLN cc_start: 0.9074 (mt0) cc_final: 0.8548 (mp10) REVERT: A 579 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8220 (mtpp) REVERT: A 607 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5599 (tt) REVERT: A 611 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8043 (tp30) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.0949 time to fit residues: 6.1778 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 0.0670 chunk 12 optimal weight: 0.3980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099823 restraints weight = 11737.006| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.12 r_work: 0.3319 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6072 Z= 0.122 Angle : 0.510 9.809 8837 Z= 0.304 Chirality : 0.039 0.631 1089 Planarity : 0.004 0.042 621 Dihedral : 21.494 167.381 2488 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 12.97 % Favored : 85.32 % 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: 0.54 (0.49), residues: 331 helix: 1.62 (0.40), residues: 174 sheet: 1.05 (1.17), residues: 10 loop : -1.30 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 152 TYR 0.012 0.002 TYR A 97 PHE 0.008 0.001 PHE A 570 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 6072) covalent geometry : angle 0.51023 / 0.30 ( 8837) hydrogen bonds : bond 0.04842 / 3.12 ( 254) hydrogen bonds : angle 3.53348 / 2.58 ( 578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8701 (mmm160) REVERT: A 248 GLN cc_start: 0.9049 (mt0) cc_final: 0.8508 (mp10) REVERT: A 579 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8216 (mtpp) REVERT: A 607 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5236 (tt) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.1023 time to fit residues: 6.1572 Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.141699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097126 restraints weight = 11755.278| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.12 r_work: 0.3273 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6072 Z= 0.170 Angle : 0.544 9.992 8837 Z= 0.321 Chirality : 0.041 0.669 1089 Planarity : 0.004 0.037 621 Dihedral : 21.419 167.193 2488 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.39 % Allowed : 12.29 % Favored : 85.32 % 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: 0.52 (0.49), residues: 331 helix: 1.63 (0.40), residues: 174 sheet: 1.15 (1.21), residues: 10 loop : -1.35 (0.56), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 556 TYR 0.016 0.003 TYR A 76 PHE 0.011 0.002 PHE A 83 TRP 0.009 0.002 TRP A 120 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 6072) covalent geometry : angle 0.54442 / 0.32 ( 8837) hydrogen bonds : bond 0.05657 / 3.58 ( 254) hydrogen bonds : angle 3.58534 / 2.63 ( 578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7720 (p90) REVERT: A 228 ARG cc_start: 0.8975 (mmm160) cc_final: 0.8596 (mmm160) REVERT: A 248 GLN cc_start: 0.9062 (mt0) cc_final: 0.8538 (mp10) REVERT: A 579 LYS cc_start: 0.8562 (mtpt) cc_final: 0.8247 (mtpp) REVERT: A 607 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5352 (tt) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.1163 time to fit residues: 7.1074 Evaluate side-chains 49 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.143091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098902 restraints weight = 11834.258| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6072 Z= 0.129 Angle : 0.513 9.721 8837 Z= 0.303 Chirality : 0.039 0.622 1089 Planarity : 0.003 0.037 621 Dihedral : 21.435 167.315 2488 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.37 % Allowed : 12.97 % Favored : 85.67 % 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: 0.57 (0.49), residues: 331 helix: 1.73 (0.40), residues: 174 sheet: 1.19 (1.21), residues: 10 loop : -1.41 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.011 0.002 TYR A 97 PHE 0.008 0.001 PHE A 570 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 6072) covalent geometry : angle 0.51256 / 0.30 ( 8837) hydrogen bonds : bond 0.04806 / 3.09 ( 254) hydrogen bonds : angle 3.53339 / 2.59 ( 578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 662 Ramachandran restraints generated. 331 Oldfield, 0 Emsley, 331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8969 (mmm160) cc_final: 0.8693 (mmm160) REVERT: A 248 GLN cc_start: 0.9055 (mt0) cc_final: 0.8533 (mp10) REVERT: A 579 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8220 (mtpp) REVERT: A 607 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5153 (tt) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1047 time to fit residues: 6.2934 Evaluate side-chains 47 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 619 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.145024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101365 restraints weight = 11668.615| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.12 r_work: 0.3356 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6072 Z= 0.128 Angle : 0.508 9.521 8837 Z= 0.300 Chirality : 0.039 0.611 1089 Planarity : 0.003 0.037 621 Dihedral : 21.387 166.271 2488 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.71 % Allowed : 12.97 % Favored : 85.32 % 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: 0.63 (0.49), residues: 331 helix: 1.86 (0.41), residues: 173 sheet: 0.80 (1.12), residues: 10 loop : -1.44 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 198 TYR 0.011 0.002 TYR A 76 PHE 0.008 0.001 PHE A 236 TRP 0.007 0.001 TRP A 120 HIS 0.002 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 6072) covalent geometry : angle 0.50771 / 0.30 ( 8837) hydrogen bonds : bond 0.04794 / 3.08 ( 254) hydrogen bonds : angle 3.51186 / 2.58 ( 578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1475.73 seconds wall clock time: 26 minutes 3.17 seconds (1563.17 seconds total)