Starting phenix.real_space_refine on Sat May 10 01:14:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.map" model { file = "/net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mga_48244/05_2025/9mga_48244.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.033 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: 3 Type Number sf(0) Gaussians C 3423 2.51 5 N 525 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4599 Number of models: 1 Model: "" Number of chains: 3 Chain: "0" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 0 1 " pdbres="PHE 0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L 1 1 " pdbres="PHE 1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 2 1 " pdbres="PHE 2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: 3, 6, 9, AA, C, F, I, L, O, R, U, X, c, f, i, l, o, r, u, x, 4, 7, A, D, G, J, M, P, S, V, Y, a, d, g, j, m, p, s, v, y, 5, 8, B, E, H, K, N, Q, T, W, Z, b, e, h, k, n, q, t, w, z Time building chain proxies: 1.90, per 1000 atoms: 0.41 Number of scatterers: 4599 At special positions: 0 Unit cell: (81.03, 82.14, 57.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 651 8.00 N 525 7.00 C 3423 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=63, symmetry=0 Number of additional bonds: simple=63, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 321.4 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.27: 588 1.27 - 1.38: 2216 1.38 - 1.49: 892 1.49 - 1.60: 1092 1.60 - 1.71: 63 Bond restraints: 4851 Sorted by residual: bond pdb=" C02 I7L c 1 " pdb=" C04 I7L c 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L S 1 " pdb=" C04 I7L S 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L x 1 " pdb=" C04 I7L x 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L G 1 " pdb=" C04 I7L G 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C02 I7L R 1 " pdb=" C04 I7L R 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.29e+01 ... (remaining 4846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 6132 5.16 - 10.32: 189 10.32 - 15.48: 21 15.48 - 20.63: 21 20.63 - 25.79: 63 Bond angle restraints: 6426 Sorted by residual: angle pdb=" C04 I7L n 1 " pdb=" C02 I7L n 1 " pdb=" O01 I7L n 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L T 1 " pdb=" C02 I7L T 1 " pdb=" O01 I7L T 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L 5 1 " pdb=" C02 I7L 5 1 " pdb=" O01 I7L 5 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L h 1 " pdb=" C02 I7L h 1 " pdb=" O01 I7L h 1 " ideal model delta sigma weight residual 115.75 89.97 25.78 3.00e+00 1.11e-01 7.38e+01 angle pdb=" C04 I7L Q 1 " pdb=" C02 I7L Q 1 " pdb=" O01 I7L Q 1 " ideal model delta sigma weight residual 115.75 89.98 25.77 3.00e+00 1.11e-01 7.38e+01 ... (remaining 6421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 1764 14.13 - 28.27: 273 28.27 - 42.40: 63 42.40 - 56.53: 84 56.53 - 70.67: 21 Dihedral angle restraints: 2205 sinusoidal: 1071 harmonic: 1134 Sorted by residual: dihedral pdb=" N PHE O 2 " pdb=" C PHE O 2 " pdb=" CA PHE O 2 " pdb=" CB PHE O 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE L 2 " pdb=" C PHE L 2 " pdb=" CA PHE L 2 " pdb=" CB PHE L 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE f 2 " pdb=" C PHE f 2 " pdb=" CA PHE f 2 " pdb=" CB PHE f 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 2202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 252 0.054 - 0.107: 42 0.107 - 0.161: 0 0.161 - 0.215: 42 0.215 - 0.268: 21 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA PHE I 2 " pdb=" N PHE I 2 " pdb=" C PHE I 2 " pdb=" CB PHE I 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE R 2 " pdb=" N PHE R 2 " pdb=" C PHE R 2 " pdb=" CB PHE R 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE F 2 " pdb=" N PHE F 2 " pdb=" C PHE F 2 " pdb=" CB PHE F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 354 not shown) Planarity restraints: 777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE y 3 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE y 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE y 3 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE y 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE y 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE y 3 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE y 3 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE p 3 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.13e+00 pdb=" CG PHE p 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE p 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE p 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE p 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE p 3 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE p 3 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 3 " -0.020 2.00e-02 2.50e+03 2.15e-02 8.12e+00 pdb=" CG PHE P 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE P 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE P 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE P 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 3 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE P 3 " -0.013 2.00e-02 2.50e+03 ... (remaining 774 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 2592 3.02 - 3.49: 2724 3.49 - 3.96: 5947 3.96 - 4.43: 8231 4.43 - 4.90: 13054 Nonbonded interactions: 32548 Sorted by model distance: nonbonded pdb=" O PHE P 2 " pdb=" O PHE Y 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 4 2 " pdb=" O PHE d 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 1 2 " pdb=" O PHE a 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 7 2 " pdb=" O PHE g 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE A 2 " pdb=" O PHE M 3 " model vdw 2.556 3.040 ... (remaining 32543 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: 0.02 Found NCS groups: ncs_group { reference = (chain '0' and resid 1 through 7) selection = chain '1' selection = (chain '2' and resid 1 through 7) selection = (chain '3' and resid 1 through 7) selection = chain '4' selection = (chain '5' and resid 1 through 7) selection = (chain '6' and resid 1 through 7) selection = chain '7' selection = (chain '8' and resid 1 through 7) selection = (chain '9' and resid 1 through 7) selection = chain 'A' selection = (chain 'AA' and resid 1 through 7) selection = (chain 'B' and resid 1 through 7) selection = (chain 'C' and resid 1 through 7) selection = chain 'D' selection = (chain 'E' and resid 1 through 7) selection = (chain 'F' and resid 1 through 7) selection = chain 'G' selection = (chain 'H' and resid 1 through 7) selection = (chain 'I' and resid 1 through 7) selection = chain 'J' selection = (chain 'K' and resid 1 through 7) selection = (chain 'L' and resid 1 through 7) selection = chain 'M' selection = (chain 'N' and resid 1 through 7) selection = (chain 'O' and resid 1 through 7) selection = chain 'P' selection = (chain 'Q' and resid 1 through 7) selection = (chain 'R' and resid 1 through 7) selection = chain 'S' selection = (chain 'T' and resid 1 through 7) selection = (chain 'U' and resid 1 through 7) selection = chain 'V' selection = (chain 'W' and resid 1 through 7) selection = (chain 'X' and resid 1 through 7) selection = chain 'Y' selection = (chain 'Z' and resid 1 through 7) selection = chain 'a' selection = (chain 'b' and resid 1 through 7) selection = (chain 'c' and resid 1 through 7) selection = chain 'd' selection = (chain 'e' and resid 1 through 7) selection = (chain 'f' and resid 1 through 7) selection = chain 'g' selection = (chain 'h' and resid 1 through 7) selection = (chain 'i' and resid 1 through 7) selection = chain 'j' selection = (chain 'k' and resid 1 through 7) selection = (chain 'l' and resid 1 through 7) selection = chain 'm' selection = (chain 'n' and resid 1 through 7) selection = (chain 'o' and resid 1 through 7) selection = chain 'p' selection = (chain 'q' and resid 1 through 7) selection = (chain 'r' and resid 1 through 7) selection = chain 's' selection = (chain 't' and resid 1 through 7) selection = (chain 'u' and resid 1 through 7) selection = chain 'v' selection = (chain 'w' and resid 1 through 7) selection = (chain 'x' and resid 1 through 7) selection = chain 'y' selection = (chain 'z' and resid 1 through 7) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.650 Find NCS groups from input model: 0.340 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.035 0.159 4914 Z= 1.867 Angle : 3.300 25.793 6426 Z= 1.434 Chirality : 0.094 0.268 357 Planarity : 0.016 0.062 777 Dihedral : 18.894 70.665 1491 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.88 % Allowed : 11.76 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.19), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.15), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.047 0.011 PHE y 3 TYR 0.005 0.002 TYR 1 7 Details of bonding type rmsd covalent geometry : bond 0.03489 ( 4851) covalent geometry : angle 3.29981 ( 6426) Misc. bond : bond 0.02035 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.447 Fit side-chains REVERT: D 7 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: M 7 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: V 7 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: 4 7 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: 7 7 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: j 7 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6029 (m-80) outliers start: 21 outliers final: 3 residues processed: 53 average time/residue: 0.9186 time to fit residues: 51.5778 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 7 TYR Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain s residue 7 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN E 8 GLN H 8 GLN K 8 GLN N 8 GLN T 8 GLN W 8 GLN Z 8 GLN 2 8 GLN 5 8 GLN 8 8 GLN b 8 GLN e 8 GLN h 8 GLN k 8 GLN n 8 GLN q 8 GLN t 8 GLN w 8 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.056569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.045748 restraints weight = 11288.313| |-----------------------------------------------------------------------------| r_work (start): 0.2500 rms_B_bonded: 2.44 r_work: 0.2397 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.135 0.725 4914 Z= 5.374 Angle : 4.627 31.782 6426 Z= 2.422 Chirality : 0.286 0.722 357 Planarity : 0.036 0.144 777 Dihedral : 24.214 84.677 627 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 2.38 % Allowed : 18.03 % Favored : 79.59 % Rotamer: Outliers : 7.84 % Allowed : 5.04 % Favored : 87.11 % Cbeta Deviations : 8.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.11 % Twisted General : 6.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.29), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.22), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.123 0.026 PHE 7 3 TYR 0.111 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13585 ( 4851) covalent geometry : angle 4.62693 ( 6426) Misc. bond : bond 0.00967 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.475 Fit side-chains REVERT: J 6 GLN cc_start: 0.8801 (pt0) cc_final: 0.8590 (pt0) REVERT: O 8 GLN cc_start: 0.8252 (mt0) cc_final: 0.7034 (tm-30) REVERT: Q 8 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: U 8 GLN cc_start: 0.7936 (mt0) cc_final: 0.6954 (tm-30) REVERT: 2 8 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8341 (mp10) REVERT: 3 8 GLN cc_start: 0.8058 (mt0) cc_final: 0.7196 (tm-30) REVERT: 5 8 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8389 (mm110) REVERT: 9 8 GLN cc_start: 0.7995 (mt0) cc_final: 0.6876 (tm-30) REVERT: c 8 GLN cc_start: 0.8431 (mt0) cc_final: 0.7750 (tm-30) REVERT: i 8 GLN cc_start: 0.8362 (mt0) cc_final: 0.7576 (tm-30) REVERT: j 7 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: m 7 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: y 6 GLN cc_start: 0.8842 (pt0) cc_final: 0.7848 (pp30) outliers start: 28 outliers final: 16 residues processed: 74 average time/residue: 1.5854 time to fit residues: 120.7115 Evaluate side-chains 69 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN E 8 GLN N 8 GLN T 8 GLN a 6 GLN h 8 GLN k 8 GLN p 6 GLN q 8 GLN s 6 GLN w 8 GLN z 8 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.045225 restraints weight = 11148.608| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.46 r_work: 0.2395 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.135 0.749 4914 Z= 5.380 Angle : 4.622 30.166 6426 Z= 2.438 Chirality : 0.287 0.697 357 Planarity : 0.037 0.157 777 Dihedral : 23.411 81.079 625 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 21.43 % Favored : 78.23 % Rotamer: Outliers : 9.24 % Allowed : 10.92 % Favored : 79.83 % Cbeta Deviations : 9.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.24), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.124 0.027 PHE P 3 TYR 0.127 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13604 ( 4851) covalent geometry : angle 4.62224 ( 6426) Misc. bond : bond 0.00925 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.485 Fit side-chains REVERT: A 6 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: L 8 GLN cc_start: 0.8133 (mt0) cc_final: 0.7569 (tm130) REVERT: Q 8 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: U 8 GLN cc_start: 0.7989 (mt0) cc_final: 0.7038 (tm-30) REVERT: W 8 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: 2 8 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: 3 8 GLN cc_start: 0.8068 (mt0) cc_final: 0.7139 (tm-30) REVERT: 6 8 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: 9 8 GLN cc_start: 0.8022 (mt0) cc_final: 0.6929 (tm-30) REVERT: b 8 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7298 (mm-40) REVERT: c 8 GLN cc_start: 0.8225 (mt0) cc_final: 0.7620 (tm-30) REVERT: i 8 GLN cc_start: 0.8378 (mt0) cc_final: 0.7538 (tm-30) REVERT: j 7 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: l 8 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: m 7 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: n 8 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: w 8 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8298 (mm110) REVERT: y 6 GLN cc_start: 0.8819 (pt0) cc_final: 0.7865 (pp30) outliers start: 33 outliers final: 20 residues processed: 71 average time/residue: 1.6449 time to fit residues: 120.2203 Evaluate side-chains 75 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain R residue 5 PRO Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN Q 8 GLN a 6 GLN k 8 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.045372 restraints weight = 11074.178| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.42 r_work: 0.2395 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.782 4914 Z= 5.389 Angle : 4.657 30.471 6426 Z= 2.461 Chirality : 0.285 0.724 357 Planarity : 0.037 0.159 777 Dihedral : 23.389 80.662 625 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 1.02 % Allowed : 21.09 % Favored : 77.89 % Rotamer: Outliers : 9.80 % Allowed : 11.76 % Favored : 78.43 % Cbeta Deviations : 9.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.76 (0.30), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.126 0.027 PHE P 3 TYR 0.129 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13643 ( 4851) covalent geometry : angle 4.65704 ( 6426) Misc. bond : bond 0.00910 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 0.459 Fit side-chains REVERT: A 6 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8590 (pt0) REVERT: L 8 GLN cc_start: 0.8375 (mt0) cc_final: 0.7588 (tm130) REVERT: U 8 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: W 8 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: 2 8 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: 3 8 GLN cc_start: 0.8227 (mt0) cc_final: 0.7339 (tm-30) REVERT: 6 8 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: 9 8 GLN cc_start: 0.8068 (mt0) cc_final: 0.6997 (tm-30) REVERT: c 8 GLN cc_start: 0.8225 (mt0) cc_final: 0.7764 (tt0) REVERT: i 8 GLN cc_start: 0.8391 (mt0) cc_final: 0.7530 (tm-30) REVERT: j 7 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: l 8 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: m 7 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: n 8 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7451 (mm-40) REVERT: p 7 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: q 6 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9151 (tt0) REVERT: y 6 GLN cc_start: 0.8810 (pt0) cc_final: 0.7928 (pp30) outliers start: 35 outliers final: 20 residues processed: 70 average time/residue: 1.5492 time to fit residues: 111.6779 Evaluate side-chains 76 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN k 8 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.056111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.045108 restraints weight = 11343.140| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.49 r_work: 0.2393 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2272 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.135 0.752 4914 Z= 5.385 Angle : 4.650 30.406 6426 Z= 2.453 Chirality : 0.287 0.726 357 Planarity : 0.037 0.159 777 Dihedral : 23.394 80.787 625 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 21.77 % Favored : 77.55 % Rotamer: Outliers : 11.20 % Allowed : 12.32 % Favored : 76.47 % Cbeta Deviations : 9.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 8.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.130 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13632 ( 4851) covalent geometry : angle 4.64973 ( 6426) Misc. bond : bond 0.00902 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 45 time to evaluate : 0.491 Fit side-chains REVERT: A 6 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: L 8 GLN cc_start: 0.8366 (mt0) cc_final: 0.7612 (tm130) REVERT: Q 8 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: U 8 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: W 8 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: 2 8 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: 3 8 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: 6 8 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: 9 8 GLN cc_start: 0.8060 (mt0) cc_final: 0.6975 (tm-30) REVERT: b 8 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7277 (mm-40) REVERT: c 8 GLN cc_start: 0.8223 (mt0) cc_final: 0.7759 (tt0) REVERT: i 8 GLN cc_start: 0.8379 (mt0) cc_final: 0.7497 (tm-30) REVERT: j 7 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: l 8 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: m 7 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: p 7 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: q 6 GLN cc_start: 0.9441 (OUTLIER) cc_final: 0.9166 (tt0) REVERT: y 6 GLN cc_start: 0.8812 (pt0) cc_final: 0.7935 (pp30) outliers start: 40 outliers final: 21 residues processed: 72 average time/residue: 1.6306 time to fit residues: 120.7347 Evaluate side-chains 79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN k 8 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.045243 restraints weight = 11109.606| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.43 r_work: 0.2397 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2277 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.777 4914 Z= 5.388 Angle : 4.661 30.422 6426 Z= 2.462 Chirality : 0.287 0.727 357 Planarity : 0.037 0.159 777 Dihedral : 23.454 81.073 625 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 1.02 % Allowed : 21.77 % Favored : 77.21 % Rotamer: Outliers : 11.76 % Allowed : 12.04 % Favored : 76.19 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 8.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.76 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.133 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13643 ( 4851) covalent geometry : angle 4.66098 ( 6426) Misc. bond : bond 0.00898 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 46 time to evaluate : 0.533 Fit side-chains REVERT: A 6 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: L 8 GLN cc_start: 0.8353 (mt0) cc_final: 0.7532 (tm130) REVERT: Q 8 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: U 8 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: W 8 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: 2 8 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: 3 8 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: 6 8 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: 8 8 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: 9 8 GLN cc_start: 0.8046 (mt0) cc_final: 0.6976 (tm-30) REVERT: c 8 GLN cc_start: 0.8222 (mt0) cc_final: 0.7764 (tt0) REVERT: d 7 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: i 8 GLN cc_start: 0.8373 (mt0) cc_final: 0.7509 (tm-30) REVERT: j 7 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: l 8 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: m 7 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: n 8 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: p 7 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: q 6 GLN cc_start: 0.9435 (OUTLIER) cc_final: 0.9158 (tt0) REVERT: y 6 GLN cc_start: 0.8791 (pt0) cc_final: 0.7928 (pp30) outliers start: 42 outliers final: 22 residues processed: 76 average time/residue: 1.6467 time to fit residues: 128.6553 Evaluate side-chains 83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 46 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain 8 residue 8 GLN Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain d residue 7 TYR Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.045365 restraints weight = 11013.342| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.42 r_work: 0.2400 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.775 4914 Z= 5.387 Angle : 4.661 30.413 6426 Z= 2.463 Chirality : 0.287 0.732 357 Planarity : 0.037 0.159 777 Dihedral : 23.462 80.589 625 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.68 % Allowed : 22.11 % Favored : 77.21 % Rotamer: Outliers : 11.20 % Allowed : 11.48 % Favored : 77.31 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.77 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.39 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.131 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13641 ( 4851) covalent geometry : angle 4.66078 ( 6426) Misc. bond : bond 0.00901 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 45 time to evaluate : 0.488 Fit side-chains REVERT: A 6 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: L 8 GLN cc_start: 0.8351 (mt0) cc_final: 0.7534 (tm130) REVERT: Q 8 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8568 (mp10) REVERT: U 8 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: W 8 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: 2 8 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: 3 8 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: 6 8 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: 9 8 GLN cc_start: 0.8046 (mt0) cc_final: 0.6959 (tm-30) REVERT: b 8 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7242 (mm-40) REVERT: c 8 GLN cc_start: 0.8199 (mt0) cc_final: 0.7744 (tt0) REVERT: i 8 GLN cc_start: 0.8378 (mt0) cc_final: 0.7502 (tm-30) REVERT: j 7 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: l 8 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: m 7 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: p 7 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: q 6 GLN cc_start: 0.9436 (OUTLIER) cc_final: 0.9159 (tt0) REVERT: y 6 GLN cc_start: 0.8801 (pt0) cc_final: 0.7957 (pp30) outliers start: 40 outliers final: 21 residues processed: 71 average time/residue: 1.6256 time to fit residues: 118.6728 Evaluate side-chains 79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.056239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.045316 restraints weight = 11349.174| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.45 r_work: 0.2399 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2278 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.782 4914 Z= 5.389 Angle : 4.664 30.411 6426 Z= 2.463 Chirality : 0.287 0.734 357 Planarity : 0.037 0.158 777 Dihedral : 23.470 80.983 625 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.68 % Allowed : 22.11 % Favored : 77.21 % Rotamer: Outliers : 11.48 % Allowed : 10.36 % Favored : 78.15 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 8.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.132 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13647 ( 4851) covalent geometry : angle 4.66392 ( 6426) Misc. bond : bond 0.00885 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 46 time to evaluate : 0.491 Fit side-chains REVERT: A 6 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: L 8 GLN cc_start: 0.8349 (mt0) cc_final: 0.7505 (tm130) REVERT: P 6 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: Q 8 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: U 8 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: W 8 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: 2 8 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: 3 8 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: 6 8 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: 8 8 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: 9 8 GLN cc_start: 0.8039 (mt0) cc_final: 0.6966 (tm-30) REVERT: b 8 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7247 (mm-40) REVERT: i 8 GLN cc_start: 0.8372 (mt0) cc_final: 0.7497 (tm-30) REVERT: j 7 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: l 8 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: m 7 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: n 8 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7419 (mm-40) REVERT: p 7 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: q 6 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9161 (tt0) REVERT: y 6 GLN cc_start: 0.8795 (pt0) cc_final: 0.7959 (pp30) outliers start: 41 outliers final: 22 residues processed: 74 average time/residue: 1.6296 time to fit residues: 124.0070 Evaluate side-chains 84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 46 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain 8 residue 8 GLN Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.056116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.045136 restraints weight = 11138.073| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.47 r_work: 0.2395 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2272 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.781 4914 Z= 5.389 Angle : 4.663 30.406 6426 Z= 2.464 Chirality : 0.287 0.735 357 Planarity : 0.037 0.159 777 Dihedral : 23.469 80.736 625 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.68 % Allowed : 22.11 % Favored : 77.21 % Rotamer: Outliers : 11.76 % Allowed : 10.08 % Favored : 78.15 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.79 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.41 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.132 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13646 ( 4851) covalent geometry : angle 4.66309 ( 6426) Misc. bond : bond 0.00911 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 45 time to evaluate : 0.495 Fit side-chains REVERT: A 6 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: L 8 GLN cc_start: 0.8358 (mt0) cc_final: 0.7496 (tm130) REVERT: P 6 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: Q 8 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: U 8 GLN cc_start: 0.7975 (tt0) cc_final: 0.6920 (tm-30) REVERT: W 8 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: 2 8 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: 3 8 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: 6 8 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: 8 8 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: 9 8 GLN cc_start: 0.8042 (mt0) cc_final: 0.6949 (tm-30) REVERT: b 8 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7250 (mm-40) REVERT: i 8 GLN cc_start: 0.8386 (mt0) cc_final: 0.7488 (tm-30) REVERT: j 7 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: l 8 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: m 7 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: p 7 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: q 6 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9169 (tt0) REVERT: y 6 GLN cc_start: 0.8807 (pt0) cc_final: 0.7952 (pp30) outliers start: 42 outliers final: 24 residues processed: 73 average time/residue: 1.6532 time to fit residues: 124.1015 Evaluate side-chains 83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain 8 residue 8 GLN Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 6 GLN Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN p 6 GLN q 8 GLN z 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.045208 restraints weight = 11077.770| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 2.43 r_work: 0.2401 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2280 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.779 4914 Z= 5.389 Angle : 4.667 30.403 6426 Z= 2.464 Chirality : 0.288 0.735 357 Planarity : 0.037 0.158 777 Dihedral : 23.474 80.860 625 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.68 % Allowed : 22.11 % Favored : 77.21 % Rotamer: Outliers : 10.64 % Allowed : 11.20 % Favored : 78.15 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.81 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.132 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13646 ( 4851) covalent geometry : angle 4.66692 ( 6426) Misc. bond : bond 0.00884 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 45 time to evaluate : 0.487 Fit side-chains REVERT: A 6 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: L 8 GLN cc_start: 0.8351 (mt0) cc_final: 0.7503 (tm130) REVERT: P 6 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: Q 8 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: U 8 GLN cc_start: 0.7974 (tt0) cc_final: 0.6941 (tm-30) REVERT: W 8 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: 2 8 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7564 (mt0) REVERT: 3 8 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: 6 8 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: 8 8 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: 9 8 GLN cc_start: 0.8040 (mt0) cc_final: 0.6974 (tm-30) REVERT: b 8 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7262 (mm-40) REVERT: i 8 GLN cc_start: 0.8377 (mt0) cc_final: 0.7491 (tm-30) REVERT: j 7 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: l 8 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: m 7 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: p 7 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: q 6 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9162 (tt0) REVERT: y 6 GLN cc_start: 0.8794 (pt0) cc_final: 0.7957 (pp30) outliers start: 38 outliers final: 22 residues processed: 72 average time/residue: 1.5942 time to fit residues: 118.4726 Evaluate side-chains 81 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 45 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 7 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 7 TYR Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain S residue 6 GLN Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain W residue 8 GLN Chi-restraints excluded: chain Y residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 2 residue 8 GLN Chi-restraints excluded: chain 3 residue 8 GLN Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 6 residue 8 GLN Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain 8 residue 8 GLN Chi-restraints excluded: chain a residue 7 TYR Chi-restraints excluded: chain b residue 6 GLN Chi-restraints excluded: chain b residue 8 GLN Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain l residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain m residue 7 TYR Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 8 GLN Chi-restraints excluded: chain p residue 7 TYR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain s residue 7 TYR Chi-restraints excluded: chain v residue 7 TYR Chi-restraints excluded: chain y residue 5 PRO Chi-restraints excluded: chain y residue 7 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN N 8 GLN a 6 GLN p 6 GLN q 8 GLN v 6 GLN z 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.056094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.045120 restraints weight = 11215.643| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.48 r_work: 0.2396 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.136 0.781 4914 Z= 5.389 Angle : 4.664 30.399 6426 Z= 2.464 Chirality : 0.287 0.735 357 Planarity : 0.037 0.159 777 Dihedral : 23.471 80.797 625 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.68 % Allowed : 22.11 % Favored : 77.21 % Rotamer: Outliers : 10.36 % Allowed : 11.20 % Favored : 78.43 % Cbeta Deviations : 8.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.70 % Twisted General : 7.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.81 (0.31), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.23), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.125 0.027 PHE P 3 TYR 0.132 0.022 TYR I 7 Details of bonding type rmsd covalent geometry : bond 0.13646 ( 4851) covalent geometry : angle 4.66431 ( 6426) Misc. bond : bond 0.00910 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.08 seconds wall clock time: 49 minutes 35.24 seconds (2975.24 seconds total)