Starting phenix.real_space_refine on Tue Aug 4 16:37:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgu_16036/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2026/8bgu_16036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_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-2.2rc3-6140/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: {'RNAv2': 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: 1.25, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 103.4 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: 0.58 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: 0.66 Time building geometry restraints manager: 0.52 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=" 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' G 3 52 " pdb=" O3' G 3 52 " ideal model delta sigma weight residual 1.415 1.442 -0.027 2.00e-02 2.50e+03 1.81e+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=" C3' C 3 98 " pdb=" O3' C 3 98 " ideal model delta sigma weight residual 1.415 1.439 -0.024 2.00e-02 2.50e+03 1.47e+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: 6877 1.65 - 3.31: 525 3.31 - 4.96: 108 4.96 - 6.62: 20 6.62 - 8.27: 9 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=" C3' G 3 52 " pdb=" O3' G 3 52 " pdb=" P U 3 53 " ideal model delta sigma weight residual 119.70 126.68 -6.98 1.20e+00 6.94e-01 3.38e+01 angle pdb=" C3' C 3 98 " pdb=" O3' C 3 98 " pdb=" P G 3 99 " ideal model delta sigma weight residual 119.70 126.53 -6.83 1.20e+00 6.94e-01 3.24e+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 angle pdb=" O3' G 3 52 " pdb=" C3' G 3 52 " pdb=" C2' G 3 52 " ideal model delta sigma weight residual 113.80 120.98 -7.18 2.00e+00 2.50e-01 1.29e+01 ... (remaining 7534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 2359 24.32 - 48.64: 232 48.64 - 72.97: 119 72.97 - 97.29: 3 97.29 - 121.61: 2 Dihedral angle restraints: 2715 sinusoidal: 1449 harmonic: 1266 Sorted by residual: dihedral pdb=" C4' G 3 77 " pdb=" C3' G 3 77 " pdb=" C2' G 3 77 " pdb=" C1' G 3 77 " ideal model delta sinusoidal sigma weight residual 36.34 -38.82 75.17 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' A 3 13 " pdb=" C3' A 3 13 " pdb=" C2' A 3 13 " pdb=" C1' A 3 13 " ideal model delta sinusoidal sigma weight residual 36.34 -37.63 73.98 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' U 3 54 " pdb=" C3' U 3 54 " pdb=" C2' U 3 54 " pdb=" C1' U 3 54 " ideal model delta sinusoidal sigma weight residual 36.34 -36.86 73.21 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 2712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 787 0.073 - 0.146: 78 0.146 - 0.220: 41 0.220 - 0.293: 104 0.293 - 0.366: 6 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 -2.50 -2.13 -0.37 2.00e-01 2.50e+01 3.35e+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 -2.50 -2.16 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' A 3 13 " pdb=" C4' A 3 13 " pdb=" O3' A 3 13 " pdb=" C2' A 3 13 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.32e+00 ... (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: 0.510 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.590 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.260 ------------------------------------------------------------------------------- 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 : 0.004 0.027 5079 Z= 0.200 Angle : 1.051 8.272 7539 Z= 0.485 Chirality : 0.099 0.366 1016 Planarity : 0.003 0.017 565 Dihedral : 21.220 121.608 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 0.00355 / 0.20 ( 5079) covalent geometry : angle 1.05140 / 0.49 ( 7539) hydrogen bonds : bond 0.12779 / 8.44 ( 227) hydrogen bonds : angle 5.46473 / 3.79 ( 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 : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0201 time to fit residues: 0.5836 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 : 0.065 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.043647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.030776 restraints weight = 57915.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031534 restraints weight = 33395.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032089 restraints weight = 23704.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.032448 restraints weight = 18667.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032591 restraints weight = 15951.784| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.041 5079 Z= 0.508 Angle : 1.481 14.432 7539 Z= 0.604 Chirality : 0.096 0.940 1016 Planarity : 0.005 0.015 565 Dihedral : 19.977 157.231 1893 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 33.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % 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: -1.73 (0.38), residues: 441 helix: 0.06 (0.42), residues: 143 sheet: -1.32 (0.68), residues: 54 loop : -1.91 (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 0.00939 / 0.51 ( 5079) covalent geometry : angle 1.48072 / 0.60 ( 7539) hydrogen bonds : bond 0.12977 / 9.31 ( 227) hydrogen bonds : angle 5.20839 / 3.26 ( 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 : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0230 time to fit residues: 0.7076 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 : 0.115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.044976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.032029 restraints weight = 55875.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032845 restraints weight = 32108.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.033394 restraints weight = 22541.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033728 restraints weight = 17799.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.033992 restraints weight = 15308.057| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5079 Z= 0.286 Angle : 1.097 13.417 7539 Z= 0.450 Chirality : 0.076 0.526 1016 Planarity : 0.003 0.011 565 Dihedral : 19.844 160.968 1893 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % 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: -1.24 (0.40), residues: 441 helix: 0.88 (0.45), residues: 143 sheet: -1.42 (0.78), residues: 42 loop : -1.81 (0.37), residues: 256 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 0.00528 / 0.29 ( 5079) covalent geometry : angle 1.09681 / 0.45 ( 7539) hydrogen bonds : bond 0.08279 / 5.85 ( 227) hydrogen bonds : angle 4.41218 / 2.78 ( 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 : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0224 time to fit residues: 0.6704 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 : 0.108 ------------------------------------------------------------------------------- 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: 7.9990 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.044154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031362 restraints weight = 56674.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.032116 restraints weight = 32711.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032648 restraints weight = 22968.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.032892 restraints weight = 18121.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033213 restraints weight = 15889.318| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5079 Z= 0.313 Angle : 1.129 12.029 7539 Z= 0.463 Chirality : 0.077 0.546 1016 Planarity : 0.003 0.011 565 Dihedral : 20.080 178.827 1893 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % 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: -1.13 (0.40), residues: 441 helix: 1.35 (0.46), residues: 137 sheet: -1.41 (0.79), residues: 42 loop : -1.90 (0.37), residues: 262 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 0.00582 / 0.31 ( 5079) covalent geometry : angle 1.12935 / 0.46 ( 7539) hydrogen bonds : bond 0.09498 / 6.76 ( 227) hydrogen bonds : angle 4.52076 / 2.85 ( 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 : 0.136 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0225 time to fit residues: 0.7068 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 : 0.065 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 50 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.044107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031310 restraints weight = 55881.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.032096 restraints weight = 32508.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032658 restraints weight = 22878.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.032993 restraints weight = 17992.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.033151 restraints weight = 15378.560| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5079 Z= 0.290 Angle : 1.072 13.217 7539 Z= 0.440 Chirality : 0.075 0.523 1016 Planarity : 0.003 0.012 565 Dihedral : 20.133 179.048 1893 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.30 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: -0.89 (0.40), residues: 441 helix: 1.35 (0.45), residues: 143 sheet: -1.11 (1.03), residues: 28 loop : -1.72 (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 0.00537 / 0.29 ( 5079) covalent geometry : angle 1.07181 / 0.44 ( 7539) hydrogen bonds : bond 0.08115 / 5.75 ( 227) hydrogen bonds : angle 4.41453 / 2.77 ( 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 : 0.067 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0150 time to fit residues: 0.4458 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.043349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.030716 restraints weight = 58201.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031477 restraints weight = 32664.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.032018 restraints weight = 22729.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.032384 restraints weight = 17739.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.032613 restraints weight = 14989.924| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 5079 Z= 0.327 Angle : 1.119 13.714 7539 Z= 0.460 Chirality : 0.079 0.620 1016 Planarity : 0.003 0.012 565 Dihedral : 20.201 175.565 1893 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % 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: -1.17 (0.40), residues: 441 helix: 1.12 (0.44), residues: 142 sheet: -1.47 (0.80), residues: 40 loop : -1.86 (0.37), 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 0.00605 / 0.33 ( 5079) covalent geometry : angle 1.11920 / 0.46 ( 7539) hydrogen bonds : bond 0.09085 / 6.46 ( 227) hydrogen bonds : angle 4.65574 / 2.94 ( 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 : 0.123 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0239 time to fit residues: 0.7543 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 ------------------------------------------------------------------------------- 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: 0.0030 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 overall best weight: 9.4002 ------------------------------------------------------------------------------- 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 = 0.2980 r_free = 0.2980 target = 0.041902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.029293 restraints weight = 58763.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030082 restraints weight = 32486.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030591 restraints weight = 22237.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.030946 restraints weight = 17335.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.031148 restraints weight = 14676.861| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.038 5079 Z= 0.473 Angle : 1.316 15.270 7539 Z= 0.542 Chirality : 0.086 0.637 1016 Planarity : 0.004 0.014 565 Dihedral : 20.503 174.553 1893 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 37.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % 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: -1.88 (0.38), residues: 441 helix: 0.13 (0.43), residues: 136 sheet: -1.72 (0.98), residues: 28 loop : -2.02 (0.36), residues: 277 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 0.00875 / 0.47 ( 5079) covalent geometry : angle 1.31574 / 0.54 ( 7539) hydrogen bonds : bond 0.11401 / 8.10 ( 227) hydrogen bonds : angle 5.36572 / 3.33 ( 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 : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0238 time to fit residues: 0.7163 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 : 0.115 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 40 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 = 0.042876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.030290 restraints weight = 57884.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.031051 restraints weight = 32774.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031557 restraints weight = 22856.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.031913 restraints weight = 17914.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.032111 restraints weight = 15172.079| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 5079 Z= 0.328 Angle : 1.131 14.192 7539 Z= 0.464 Chirality : 0.079 0.585 1016 Planarity : 0.003 0.013 565 Dihedral : 20.296 174.132 1893 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % 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: -1.57 (0.39), residues: 441 helix: 0.48 (0.44), residues: 143 sheet: -1.75 (0.99), 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 0.00609 / 0.33 ( 5079) covalent geometry : angle 1.13080 / 0.46 ( 7539) hydrogen bonds : bond 0.08873 / 6.30 ( 227) hydrogen bonds : angle 4.79151 / 3.00 ( 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 : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0235 time to fit residues: 0.7136 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 : 0.114 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030158 restraints weight = 57617.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.030882 restraints weight = 32735.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.031387 restraints weight = 22799.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031731 restraints weight = 17816.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.031944 restraints weight = 15088.009| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 5079 Z= 0.353 Angle : 1.162 14.409 7539 Z= 0.476 Chirality : 0.080 0.572 1016 Planarity : 0.003 0.013 565 Dihedral : 20.243 173.820 1893 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % 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: -1.57 (0.40), residues: 441 helix: 0.52 (0.43), residues: 143 sheet: -1.90 (0.97), 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 0.00655 / 0.35 ( 5079) covalent geometry : angle 1.16184 / 0.48 ( 7539) hydrogen bonds : bond 0.09330 / 6.66 ( 227) hydrogen bonds : angle 4.94613 / 3.07 ( 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 : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0237 time to fit residues: 0.7235 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 ------------------------------------------------------------------------------- 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: 20.0000 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.3980 chunk 26 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.043079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.030593 restraints weight = 56550.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031314 restraints weight = 32204.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031824 restraints weight = 22436.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032168 restraints weight = 17567.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032307 restraints weight = 14885.612| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5079 Z= 0.291 Angle : 1.090 14.017 7539 Z= 0.445 Chirality : 0.078 0.570 1016 Planarity : 0.003 0.013 565 Dihedral : 20.172 173.624 1893 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % 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: -1.22 (0.41), residues: 441 helix: 0.97 (0.45), residues: 143 sheet: -1.84 (1.00), residues: 28 loop : -1.79 (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 0.00541 / 0.29 ( 5079) covalent geometry : angle 1.09011 / 0.45 ( 7539) hydrogen bonds : bond 0.08239 / 5.86 ( 227) hydrogen bonds : angle 4.68226 / 2.92 ( 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 : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0248 time to fit residues: 0.7417 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 : 0.110 ------------------------------------------------------------------------------- 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: 20.0000 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.043026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.030506 restraints weight = 57170.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.031252 restraints weight = 32450.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031774 restraints weight = 22628.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.032099 restraints weight = 17700.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032337 restraints weight = 15036.467| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5079 Z= 0.298 Angle : 1.096 14.096 7539 Z= 0.448 Chirality : 0.078 0.570 1016 Planarity : 0.003 0.013 565 Dihedral : 20.152 173.785 1893 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 26.12 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: -1.15 (0.41), residues: 441 helix: 1.07 (0.45), residues: 143 sheet: -1.82 (1.02), residues: 28 loop : -1.77 (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 0.00553 / 0.30 ( 5079) covalent geometry : angle 1.09620 / 0.45 ( 7539) hydrogen bonds : bond 0.08480 / 6.04 ( 227) hydrogen bonds : angle 4.67807 / 2.92 ( 526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 807.93 seconds wall clock time: 14 minutes 34.20 seconds (874.20 seconds total)