Starting phenix.real_space_refine on Thu Jul 2 01:01:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bgu_16036/07_2026/8bgu_16036.cif" } resolution = 4.1 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= 0.005 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 Zn 1 6.06 5 P 121 5.49 5 C 2457 2.51 5 N 908 2.21 5 O 1292 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: 4779 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 36} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "3" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 51} Link IDs: {'rna2p': 13, 'rna3p': 107} Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1128 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 942 Unresolved non-hydrogen dihedrals: 637 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'TYR:plan': 17, 'ASN:plan1': 11, 'ARG:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 6, 'GLU:plan': 17, 'HIS:plan': 5, 'PHE:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 420 Chain: "B" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 861 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 169} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 719 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'GLU:plan': 14, 'ASN:plan1': 6, 'ARG:plan': 17, 'PHE:plan': 8, 'TYR:plan': 6, 'HIS:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 325 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.99, per 1000 atoms: 0.21 Number of scatterers: 4779 At special positions: 0 Unit cell: (78.366, 102.723, 130.257, 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) Zn 1 29.99 P 121 15.00 O 1292 8.00 N 908 7.00 C 2457 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: 0.42 Conformation dependent library (CDL) restraints added in 126.1 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 822 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 35.1% alpha, 10.7% beta 40 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'F' and resid 298 through 302 Processing helix chain 'A' and resid 81 through 86 Proline residue: A 84 - end of helix No H-bonds generated for 'chain 'A' and resid 81 through 86' Processing helix chain 'A' and resid 94 through 114 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'B' and resid 9 through 14 removed outlier: 3.593A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.525A pdb=" N ILE B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA B 142 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 144 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing sheet with id=AA1, first strand: chain 'F' and resid 303 through 304 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 79 removed outlier: 4.751A pdb=" N ASP A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 68 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 74 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR A 66 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.559A pdb=" N GLU A 189 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 25 128 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 567 1.30 - 1.38: 1132 1.38 - 1.46: 1169 1.46 - 1.54: 1922 1.54 - 1.62: 289 Bond restraints: 5079 Sorted by residual: bond pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " ideal model delta sigma weight residual 1.417 1.442 -0.025 1.50e-02 4.44e+03 2.76e+00 bond pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.35e+00 bond pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " ideal model delta sigma weight residual 1.417 1.439 -0.022 1.50e-02 4.44e+03 2.21e+00 bond pdb=" N GLY A 87 " pdb=" CA GLY A 87 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.77e+00 bond pdb=" N1 C 3 18 " pdb=" C2 C 3 18 " ideal model delta sigma weight residual 1.397 1.420 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 5074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 7188 1.65 - 3.31: 272 3.31 - 4.96: 54 4.96 - 6.62: 18 6.62 - 8.27: 7 Bond angle restraints: 7539 Sorted by residual: angle pdb=" C GLU B 9 " pdb=" N ASN B 10 " pdb=" CA ASN B 10 " ideal model delta sigma weight residual 120.06 127.14 -7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" O3' C 3 98 " pdb=" C3' C 3 98 " pdb=" C2' C 3 98 " ideal model delta sigma weight residual 113.70 121.40 -7.70 1.50e+00 4.44e-01 2.63e+01 angle pdb=" O3' G 3 52 " pdb=" C3' G 3 52 " pdb=" C2' G 3 52 " ideal model delta sigma weight residual 113.70 120.98 -7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sigma weight residual 120.20 126.68 -6.48 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N GLY A 87 " pdb=" CA GLY A 87 " pdb=" C GLY A 87 " ideal model delta sigma weight residual 111.67 115.60 -3.93 9.20e-01 1.18e+00 1.83e+01 ... (remaining 7534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.82: 2595 32.82 - 65.64: 102 65.64 - 98.46: 15 98.46 - 131.28: 2 131.28 - 164.10: 1 Dihedral angle restraints: 2715 sinusoidal: 1449 harmonic: 1266 Sorted by residual: dihedral pdb=" O4' U 3 121 " pdb=" C1' U 3 121 " pdb=" N1 U 3 121 " pdb=" C2 U 3 121 " ideal model delta sinusoidal sigma weight residual -128.00 36.10 -164.10 1 1.70e+01 3.46e-03 6.52e+01 dihedral pdb=" CA LEU B 94 " pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C4' C 3 98 " pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " pdb=" P G 3 99 " ideal model delta sinusoidal sigma weight residual 220.00 98.39 121.61 1 3.50e+01 8.16e-04 1.19e+01 ... (remaining 2712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 926 0.069 - 0.138: 87 0.138 - 0.207: 1 0.207 - 0.276: 0 0.276 - 0.345: 2 Chirality restraints: 1016 Sorted by residual: chirality pdb=" C3' C 3 98 " pdb=" C4' C 3 98 " pdb=" O3' C 3 98 " pdb=" C2' C 3 98 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C3' G 3 52 " pdb=" C4' G 3 52 " pdb=" O3' G 3 52 " pdb=" C2' G 3 52 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1' G 3 5 " pdb=" O4' G 3 5 " pdb=" C2' G 3 5 " pdb=" N9 G 3 5 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1013 not shown) Planarity restraints: 565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 92 " -0.024 2.00e-02 2.50e+03 1.11e-02 3.40e+00 pdb=" N9 A 3 92 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 3 92 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A 3 92 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 3 92 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 3 92 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 3 92 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 3 92 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 3 67 " 0.024 2.00e-02 2.50e+03 1.01e-02 3.05e+00 pdb=" N9 G 3 67 " -0.018 2.00e-02 2.50e+03 pdb=" C8 G 3 67 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 3 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 3 67 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G 3 67 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G 3 67 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 3 67 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G 3 67 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G 3 67 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G 3 67 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 191 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ASN A 191 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 191 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 192 " 0.010 2.00e-02 2.50e+03 ... (remaining 562 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 909 2.77 - 3.30: 3973 3.30 - 3.83: 9635 3.83 - 4.37: 9745 4.37 - 4.90: 13364 Nonbonded interactions: 37626 Sorted by model distance: nonbonded pdb=" O6 G 3 1 " pdb=" O4 U 3 121 " model vdw 2.235 3.040 nonbonded pdb=" O2' G 3 77 " pdb=" O6 G 3 101 " model vdw 2.323 3.040 nonbonded pdb=" O6 G 3 67 " pdb=" O4 U 3 111 " model vdw 2.329 2.432 nonbonded pdb=" O2 U 3 81 " pdb=" N2 G 3 99 " model vdw 2.333 2.496 nonbonded pdb=" O4 U 3 81 " pdb=" O6 G 3 99 " model vdw 2.379 2.432 ... (remaining 37621 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 group one per residue 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: 0.500 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.770 Find NCS groups from input model: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.003 0.025 5079 Z= 0.188 Angle : 0.839 8.272 7539 Z= 0.452 Chirality : 0.041 0.345 1016 Planarity : 0.003 0.017 565 Dihedral : 16.171 164.097 1893 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -2.58 (0.34), residues: 441 helix: -1.54 (0.31), residues: 142 sheet: -0.77 (0.74), residues: 55 loop : -2.07 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.19 ( 5079) covalent geometry : angle 0.83860 / 0.45 ( 7539) hydrogen bonds : bond 0.12779 / 8.59 ( 227) hydrogen bonds : angle 5.46473 / 3.95 ( 526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0157 time to fit residues: 0.4579 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 overall best weight: 9.9996 ------------------------------------------------------------------------------- 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 = 0.3011 r_free = 0.3011 target = 0.043132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.030412 restraints weight = 58452.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.031219 restraints weight = 33517.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031772 restraints weight = 23332.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.032130 restraints weight = 18341.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.032348 restraints weight = 15704.655| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 5079 Z= 0.479 Angle : 0.905 6.776 7539 Z= 0.474 Chirality : 0.048 0.249 1016 Planarity : 0.005 0.016 565 Dihedral : 18.173 163.077 1893 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 34.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.86 (0.38), residues: 441 helix: -0.03 (0.42), residues: 143 sheet: -1.44 (0.68), residues: 54 loop : -1.99 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.48 ( 5079) covalent geometry : angle 0.90482 / 0.47 ( 7539) hydrogen bonds : bond 0.11555 / 8.38 ( 227) hydrogen bonds : angle 5.33297 / 3.56 ( 526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.092 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0180 time to fit residues: 0.5310 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.043277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.030859 restraints weight = 57038.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.031696 restraints weight = 32658.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.032233 restraints weight = 22641.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032619 restraints weight = 17804.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032795 restraints weight = 15136.529| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 5079 Z= 0.329 Angle : 0.685 5.838 7539 Z= 0.366 Chirality : 0.040 0.221 1016 Planarity : 0.003 0.010 565 Dihedral : 17.712 162.812 1893 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.85 (0.38), residues: 441 helix: 0.16 (0.42), residues: 149 sheet: -1.75 (0.72), residues: 49 loop : -2.08 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.33 ( 5079) covalent geometry : angle 0.68544 / 0.37 ( 7539) hydrogen bonds : bond 0.07901 / 5.65 ( 227) hydrogen bonds : angle 4.74096 / 3.15 ( 526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0224 time to fit residues: 0.6969 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 overall best weight: 7.1592 ------------------------------------------------------------------------------- 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 = 0.2982 r_free = 0.2982 target = 0.042201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.029921 restraints weight = 58729.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030704 restraints weight = 33042.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031252 restraints weight = 23097.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031496 restraints weight = 18076.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.031795 restraints weight = 15819.501| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 5079 Z= 0.359 Angle : 0.734 6.357 7539 Z= 0.391 Chirality : 0.042 0.242 1016 Planarity : 0.003 0.012 565 Dihedral : 18.093 158.921 1893 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 28.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.84 (0.38), residues: 441 helix: 0.27 (0.43), residues: 143 sheet: -1.45 (0.80), residues: 40 loop : -2.17 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.36 ( 5079) covalent geometry : angle 0.73430 / 0.39 ( 7539) hydrogen bonds : bond 0.09366 / 6.75 ( 227) hydrogen bonds : angle 4.99079 / 3.31 ( 526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0224 time to fit residues: 0.6274 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 50 optimal weight: 50.0000 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.042084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.029916 restraints weight = 57946.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030679 restraints weight = 32935.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.031212 restraints weight = 23136.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.031568 restraints weight = 18071.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031766 restraints weight = 15391.359| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 5079 Z= 0.347 Angle : 0.701 6.300 7539 Z= 0.374 Chirality : 0.041 0.229 1016 Planarity : 0.003 0.010 565 Dihedral : 17.750 160.088 1893 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.79 (0.39), residues: 441 helix: 0.25 (0.43), residues: 143 sheet: -1.54 (0.99), residues: 28 loop : -2.07 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.35 ( 5079) covalent geometry : angle 0.70061 / 0.37 ( 7539) hydrogen bonds : bond 0.08389 / 6.02 ( 227) hydrogen bonds : angle 4.94314 / 3.26 ( 526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0206 time to fit residues: 0.6443 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 16 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.042147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.030014 restraints weight = 58827.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.030812 restraints weight = 33325.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.031319 restraints weight = 23028.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031691 restraints weight = 18055.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.031935 restraints weight = 15245.441| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 5079 Z= 0.305 Angle : 0.655 5.731 7539 Z= 0.350 Chirality : 0.039 0.230 1016 Planarity : 0.003 0.010 565 Dihedral : 17.505 159.746 1893 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.67 (0.40), residues: 441 helix: 0.53 (0.44), residues: 142 sheet: -1.74 (0.80), residues: 40 loop : -2.05 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.30 ( 5079) covalent geometry : angle 0.65506 / 0.35 ( 7539) hydrogen bonds : bond 0.08093 / 5.81 ( 227) hydrogen bonds : angle 4.76894 / 3.16 ( 526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0185 time to fit residues: 0.5517 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 overall best weight: 10.0394 ------------------------------------------------------------------------------- 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 = 0.2952 r_free = 0.2952 target = 0.040920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.029099 restraints weight = 59842.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.029803 restraints weight = 34784.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030297 restraints weight = 24285.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.030629 restraints weight = 19049.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030772 restraints weight = 16178.563| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 5079 Z= 0.469 Angle : 0.846 7.031 7539 Z= 0.448 Chirality : 0.047 0.243 1016 Planarity : 0.004 0.012 565 Dihedral : 18.268 156.760 1893 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 38.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.83 % Favored : 86.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -2.25 (0.38), residues: 441 helix: -0.28 (0.42), residues: 136 sheet: -1.93 (0.77), residues: 40 loop : -2.19 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.47 ( 5079) covalent geometry : angle 0.84626 / 0.45 ( 7539) hydrogen bonds : bond 0.10865 / 7.82 ( 227) hydrogen bonds : angle 5.55522 / 3.62 ( 526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0230 time to fit residues: 0.6982 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.042701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.030463 restraints weight = 57283.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.031272 restraints weight = 32580.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.031812 restraints weight = 22564.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032195 restraints weight = 17515.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032402 restraints weight = 14764.162| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5079 Z= 0.205 Angle : 0.570 5.215 7539 Z= 0.306 Chirality : 0.036 0.222 1016 Planarity : 0.002 0.009 565 Dihedral : 17.120 159.284 1893 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.34 (0.40), residues: 441 helix: 0.94 (0.45), residues: 142 sheet: -1.73 (1.00), residues: 28 loop : -1.91 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.20 ( 5079) covalent geometry : angle 0.57020 / 0.31 ( 7539) hydrogen bonds : bond 0.06844 / 4.87 ( 227) hydrogen bonds : angle 4.46616 / 2.95 ( 526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0207 time to fit residues: 0.6474 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 6.0390 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.042069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.029997 restraints weight = 57456.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030803 restraints weight = 32715.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.031285 restraints weight = 22637.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.031656 restraints weight = 17840.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031891 restraints weight = 15090.432| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 5079 Z= 0.289 Angle : 0.634 5.479 7539 Z= 0.339 Chirality : 0.039 0.230 1016 Planarity : 0.003 0.009 565 Dihedral : 17.373 157.864 1893 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.39 (0.40), residues: 441 helix: 0.80 (0.44), residues: 143 sheet: -1.73 (1.01), residues: 28 loop : -1.91 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.29 ( 5079) covalent geometry : angle 0.63402 / 0.34 ( 7539) hydrogen bonds : bond 0.07868 / 5.64 ( 227) hydrogen bonds : angle 4.71777 / 3.10 ( 526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0226 time to fit residues: 0.6831 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 = 0.2988 r_free = 0.2988 target = 0.042014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030000 restraints weight = 57376.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030776 restraints weight = 32574.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031287 restraints weight = 22717.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031637 restraints weight = 17763.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.031793 restraints weight = 15035.436| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 5079 Z= 0.308 Angle : 0.649 5.456 7539 Z= 0.347 Chirality : 0.039 0.231 1016 Planarity : 0.003 0.009 565 Dihedral : 17.378 157.864 1893 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.47 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -1.41 (0.40), residues: 441 helix: 0.79 (0.44), residues: 143 sheet: -1.73 (1.00), residues: 28 loop : -1.92 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.31 ( 5079) covalent geometry : angle 0.64932 / 0.35 ( 7539) hydrogen bonds : bond 0.07959 / 5.70 ( 227) hydrogen bonds : angle 4.73247 / 3.12 ( 526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0230 time to fit residues: 0.6984 Evaluate side-chains 13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 3 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 0.0060 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.043882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.031187 restraints weight = 55927.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032099 restraints weight = 30078.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032673 restraints weight = 20222.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.033126 restraints weight = 15576.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.033390 restraints weight = 12912.299| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 5079 Z= 0.147 Angle : 0.497 5.095 7539 Z= 0.266 Chirality : 0.034 0.218 1016 Planarity : 0.002 0.007 565 Dihedral : 16.488 160.086 1893 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.24 % 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: -0.64 (0.42), residues: 441 helix: 1.75 (0.47), residues: 143 sheet: -1.42 (1.07), residues: 28 loop : -1.63 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR F 302 PHE 0.000 0.000 PHE A 113 TRP 0.000 0.000 TRP F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 ( 5079) covalent geometry : angle 0.49734 / 0.27 ( 7539) hydrogen bonds : bond 0.05779 / 4.10 ( 227) hydrogen bonds : angle 4.02154 / 2.68 ( 526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 798.41 seconds wall clock time: 14 minutes 22.55 seconds (862.55 seconds total)