Starting phenix.real_space_refine on Tue Aug 4 23:43:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2z_43760/08_2026/8w2z_43760.cif" } resolution = 3.37 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 170 5.49 5 S 14 5.16 5 C 4181 2.51 5 N 1414 2.21 5 O 1897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 7676 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4075 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 15, 'TRANS': 509} Chain breaks: 5 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 6, 'HIS:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 8, 'TRP:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2927 Classifications: {'RNA': 137} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 55} Link IDs: {'rna2p': 13, 'rna3p': 123} Chain: "C" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Time building chain proxies: 1.90, per 1000 atoms: 0.25 Number of scatterers: 7676 At special positions: 0 Unit cell: (89.9856, 109.149, 115.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 170 15.00 O 1897 8.00 N 1414 7.00 C 4181 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: 0.61 Conformation dependent library (CDL) restraints added in 287.9 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 36.2% alpha, 13.9% beta 68 base pairs and 113 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 42 through 75 removed outlier: 3.995A pdb=" N ASP A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 136 through 150 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.601A pdb=" N LEU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.845A pdb=" N ARG A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU A 230 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 231 " --> pdb=" O ARG A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 231' Processing helix chain 'A' and resid 232 through 239 removed outlier: 4.251A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.796A pdb=" N VAL A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.510A pdb=" N GLU A 614 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 34 removed outlier: 6.592A pdb=" N VAL A 20 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 31 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 18 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG A 33 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 16 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 311 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 312 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA3, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 673 removed outlier: 3.627A pdb=" N GLY A 656 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 694 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 661 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 692 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 733 through 734 removed outlier: 6.710A pdb=" N THR A 721 " --> pdb=" O LYS A 714 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 113 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1647 1.33 - 1.46: 2646 1.46 - 1.58: 3504 1.58 - 1.70: 337 1.70 - 1.82: 22 Bond restraints: 8156 Sorted by residual: bond pdb=" C3' DG C -12 " pdb=" O3' DG C -12 " ideal model delta sigma weight residual 1.435 1.495 -0.060 1.30e-02 5.92e+03 2.12e+01 bond pdb=" C3' DT C 5 " pdb=" C2' DT C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DG D 2 " pdb=" C2' DG D 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 bond pdb=" O4' DG D 3 " pdb=" C1' DG D 3 " ideal model delta sigma weight residual 1.420 1.390 0.030 1.10e-02 8.26e+03 7.49e+00 bond pdb=" C2' G B 142 " pdb=" C1' G B 142 " ideal model delta sigma weight residual 1.526 1.504 0.022 8.00e-03 1.56e+04 7.25e+00 ... (remaining 8151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11665 3.30 - 6.60: 110 6.60 - 9.90: 11 9.90 - 13.21: 8 13.21 - 16.51: 1 Bond angle restraints: 11795 Sorted by residual: angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 117.90 -9.70 8.00e-01 1.56e+00 1.47e+02 angle pdb=" C2' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 114.00 124.64 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C3' U B 92 " pdb=" O3' U B 92 " pdb=" P U B 93 " ideal model delta sigma weight residual 119.70 127.40 -7.70 1.20e+00 6.94e-01 4.12e+01 angle pdb=" C3' G B 142 " pdb=" O3' G B 142 " pdb=" P G B 143 " ideal model delta sigma weight residual 119.70 126.49 -6.79 1.20e+00 6.94e-01 3.20e+01 angle pdb=" O3' DC C 4 " pdb=" P DT C 5 " pdb=" OP1 DT C 5 " ideal model delta sigma weight residual 108.00 124.51 -16.51 3.00e+00 1.11e-01 3.03e+01 ... (remaining 11790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 4559 34.22 - 68.44: 434 68.44 - 102.66: 44 102.66 - 136.89: 1 136.89 - 171.11: 4 Dihedral angle restraints: 5042 sinusoidal: 3513 harmonic: 1529 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual -128.00 43.11 -171.11 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA MET A 36 " pdb=" C MET A 36 " pdb=" N ARG A 37 " pdb=" CA ARG A 37 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " pdb=" C4 G B 142 " ideal model delta sinusoidal sigma weight residual 254.00 171.54 82.46 1 1.70e+01 3.46e-03 2.89e+01 ... (remaining 5039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1434 0.180 - 0.360: 5 0.360 - 0.541: 0 0.541 - 0.721: 1 0.721 - 0.901: 1 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C1' G B 142 " pdb=" O4' G B 142 " pdb=" C2' G B 142 " pdb=" N9 G B 142 " both_signs ideal model delta sigma weight residual False 2.44 1.53 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" P DT C 5 " pdb=" OP1 DT C 5 " pdb=" OP2 DT C 5 " pdb=" O5' DT C 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C3' U B 92 " pdb=" C4' U B 92 " pdb=" O3' U B 92 " pdb=" C2' U B 92 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1438 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 142 " 0.067 2.00e-02 2.50e+03 3.10e-02 2.87e+01 pdb=" N9 G B 142 " -0.081 2.00e-02 2.50e+03 pdb=" C8 G B 142 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 142 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 142 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G B 142 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 142 " 0.019 2.00e-02 2.50e+03 pdb=" N1 G B 142 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 142 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 142 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 142 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 142 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 599 " 0.017 2.00e-02 2.50e+03 2.08e-02 7.57e+00 pdb=" CG PHE A 599 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 599 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 599 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 599 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 599 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 599 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 12 " -0.033 2.00e-02 2.50e+03 1.49e-02 6.07e+00 pdb=" N9 A B 12 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A B 12 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 12 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 12 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 12 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 12 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 12 " 0.004 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1945 2.81 - 3.33: 6619 3.33 - 3.85: 14986 3.85 - 4.38: 16598 4.38 - 4.90: 24016 Nonbonded interactions: 64164 Sorted by model distance: nonbonded pdb=" NH1 ARG A 568 " pdb=" O ARG A 569 " model vdw 2.287 3.120 nonbonded pdb=" OP2 U B 91 " pdb=" O2' U B 92 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A 560 " pdb=" OP1 A B 24 " model vdw 2.295 3.040 nonbonded pdb=" O ILE A 149 " pdb=" NH1 ARG A 152 " model vdw 2.299 3.120 nonbonded pdb=" NH2 ARG A 569 " pdb=" OG SER A 627 " model vdw 2.305 3.120 ... (remaining 64159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.005 0.060 8156 Z= 0.370 Angle : 0.998 16.507 11795 Z= 0.747 Chirality : 0.066 0.901 1441 Planarity : 0.007 0.075 882 Dihedral : 22.003 171.107 4048 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.21 % Allowed : 19.61 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.35), residues: 513 helix: -0.51 (0.36), residues: 179 sheet: -0.84 (0.61), residues: 56 loop : -1.55 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 152 TYR 0.012 0.002 TYR A 169 PHE 0.048 0.003 PHE A 599 TRP 0.030 0.006 TRP A 452 HIS 0.012 0.002 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.37 ( 8156) covalent geometry : angle 0.99792 / 0.75 (11795) hydrogen bonds : bond 0.11310 / 7.74 ( 330) hydrogen bonds : angle 5.11272 / 3.53 ( 767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7939 (tt0) cc_final: 0.7706 (tt0) REVERT: A 294 ASN cc_start: 0.8924 (m-40) cc_final: 0.8513 (t0) REVERT: A 456 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8398 (tmm-80) REVERT: A 591 LYS cc_start: 0.7214 (tttt) cc_final: 0.5988 (pptt) outliers start: 5 outliers final: 1 residues processed: 58 average time/residue: 0.1122 time to fit residues: 8.5812 Evaluate side-chains 51 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097317 restraints weight = 14861.052| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.96 r_work: 0.3098 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8156 Z= 0.295 Angle : 0.721 9.856 11795 Z= 0.404 Chirality : 0.049 0.481 1441 Planarity : 0.005 0.041 882 Dihedral : 22.868 170.127 3043 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.36 % Allowed : 15.98 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.36), residues: 513 helix: 0.29 (0.37), residues: 180 sheet: -0.74 (0.68), residues: 49 loop : -1.64 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 568 TYR 0.016 0.002 TYR A 169 PHE 0.034 0.002 PHE A 648 TRP 0.018 0.004 TRP A 452 HIS 0.005 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.30 ( 8156) covalent geometry : angle 0.72145 / 0.40 (11795) hydrogen bonds : bond 0.06392 / 4.38 ( 330) hydrogen bonds : angle 4.31565 / 2.99 ( 767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3781 (OUTLIER) cc_final: 0.3535 (tm-30) REVERT: A 591 LYS cc_start: 0.7432 (tttt) cc_final: 0.6384 (pptt) outliers start: 18 outliers final: 6 residues processed: 72 average time/residue: 0.1200 time to fit residues: 11.0608 Evaluate side-chains 55 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 704 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.140513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094750 restraints weight = 14830.959| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.13 r_work: 0.3162 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8156 Z= 0.160 Angle : 0.593 10.312 11795 Z= 0.344 Chirality : 0.042 0.440 1441 Planarity : 0.004 0.035 882 Dihedral : 22.849 172.942 3043 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.66 % Allowed : 17.43 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.37), residues: 513 helix: 0.85 (0.39), residues: 180 sheet: -0.78 (0.68), residues: 49 loop : -1.55 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 568 TYR 0.008 0.001 TYR A 670 PHE 0.013 0.002 PHE A 648 TRP 0.009 0.003 TRP A 452 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 8156) covalent geometry : angle 0.59307 / 0.34 (11795) hydrogen bonds : bond 0.05180 / 3.54 ( 330) hydrogen bonds : angle 3.89945 / 2.73 ( 767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.203 Fit side-chains REVERT: A 185 GLU cc_start: 0.3539 (OUTLIER) cc_final: 0.3269 (tm-30) REVERT: A 591 LYS cc_start: 0.7403 (tttt) cc_final: 0.6510 (pptt) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.1229 time to fit residues: 9.3074 Evaluate side-chains 54 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.135555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094289 restraints weight = 15064.015| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.98 r_work: 0.3040 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 8156 Z= 0.325 Angle : 0.766 10.512 11795 Z= 0.419 Chirality : 0.053 0.547 1441 Planarity : 0.006 0.049 882 Dihedral : 22.880 167.471 3043 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.36 % Allowed : 18.16 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.36), residues: 513 helix: 0.79 (0.39), residues: 180 sheet: -1.05 (0.63), residues: 55 loop : -2.00 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 568 TYR 0.017 0.002 TYR A 169 PHE 0.031 0.003 PHE A 648 TRP 0.018 0.005 TRP A 452 HIS 0.008 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.32 ( 8156) covalent geometry : angle 0.76650 / 0.42 (11795) hydrogen bonds : bond 0.06962 / 4.65 ( 330) hydrogen bonds : angle 3.98475 / 2.77 ( 767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.204 Fit side-chains REVERT: A 15 TYR cc_start: 0.8421 (m-80) cc_final: 0.8031 (m-80) REVERT: A 185 GLU cc_start: 0.3890 (OUTLIER) cc_final: 0.3587 (tm-30) REVERT: A 591 LYS cc_start: 0.7665 (tttt) cc_final: 0.5896 (tmmt) REVERT: A 598 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8387 (ttm170) REVERT: A 735 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8580 (m) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.1180 time to fit residues: 10.0928 Evaluate side-chains 63 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.139182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093114 restraints weight = 15017.754| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.22 r_work: 0.3113 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8156 Z= 0.133 Angle : 0.552 8.959 11795 Z= 0.327 Chirality : 0.040 0.426 1441 Planarity : 0.004 0.034 882 Dihedral : 22.925 173.851 3043 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.66 % Allowed : 20.82 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.38), residues: 513 helix: 1.12 (0.39), residues: 181 sheet: -1.09 (0.62), residues: 56 loop : -1.70 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 453 TYR 0.007 0.001 TYR A 11 PHE 0.009 0.001 PHE A 263 TRP 0.011 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 8156) covalent geometry : angle 0.55205 / 0.33 (11795) hydrogen bonds : bond 0.04802 / 3.30 ( 330) hydrogen bonds : angle 3.65713 / 2.57 ( 767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.206 Fit side-chains REVERT: A 185 GLU cc_start: 0.3403 (OUTLIER) cc_final: 0.3066 (tm-30) REVERT: A 203 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 574 GLU cc_start: 0.7200 (tp30) cc_final: 0.6542 (tp30) REVERT: A 591 LYS cc_start: 0.7669 (tttt) cc_final: 0.6444 (pptt) REVERT: A 598 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8381 (ttm170) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.1307 time to fit residues: 10.2254 Evaluate side-chains 58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091113 restraints weight = 14964.051| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.22 r_work: 0.3080 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8156 Z= 0.203 Angle : 0.598 9.427 11795 Z= 0.344 Chirality : 0.044 0.460 1441 Planarity : 0.004 0.037 882 Dihedral : 22.847 169.634 3043 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.87 % Allowed : 18.64 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.37), residues: 513 helix: 1.18 (0.40), residues: 181 sheet: -1.26 (0.57), residues: 61 loop : -1.79 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 453 TYR 0.010 0.001 TYR A 169 PHE 0.018 0.002 PHE A 648 TRP 0.014 0.003 TRP A 452 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 ( 8156) covalent geometry : angle 0.59791 / 0.34 (11795) hydrogen bonds : bond 0.05329 / 3.60 ( 330) hydrogen bonds : angle 3.63609 / 2.53 ( 767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.199 Fit side-chains REVERT: A 185 GLU cc_start: 0.3594 (OUTLIER) cc_final: 0.2554 (tm-30) REVERT: A 203 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 591 LYS cc_start: 0.7816 (tttt) cc_final: 0.6262 (tmmt) REVERT: A 735 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8434 (m) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.1186 time to fit residues: 9.8834 Evaluate side-chains 63 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.136321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089835 restraints weight = 14833.150| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.18 r_work: 0.3053 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8156 Z= 0.242 Angle : 0.647 9.750 11795 Z= 0.365 Chirality : 0.046 0.488 1441 Planarity : 0.004 0.038 882 Dihedral : 22.909 169.251 3043 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.12 % Allowed : 18.64 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.37), residues: 513 helix: 1.09 (0.40), residues: 180 sheet: -1.05 (0.59), residues: 58 loop : -1.92 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 568 TYR 0.010 0.002 TYR A 169 PHE 0.020 0.002 PHE A 648 TRP 0.015 0.003 TRP A 452 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 ( 8156) covalent geometry : angle 0.64687 / 0.36 (11795) hydrogen bonds : bond 0.05649 / 3.81 ( 330) hydrogen bonds : angle 3.71363 / 2.58 ( 767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8388 (m-80) cc_final: 0.7975 (m-80) REVERT: A 185 GLU cc_start: 0.3617 (OUTLIER) cc_final: 0.2627 (tm-30) REVERT: A 203 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8332 (tm-30) REVERT: A 574 GLU cc_start: 0.7077 (tp30) cc_final: 0.6774 (tp30) REVERT: A 598 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8292 (mtm-85) REVERT: A 610 LYS cc_start: 0.7651 (tptp) cc_final: 0.7449 (tptp) REVERT: A 735 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8436 (m) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.1027 time to fit residues: 8.9626 Evaluate side-chains 67 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094139 restraints weight = 14964.820| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.18 r_work: 0.3138 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8156 Z= 0.121 Angle : 0.530 8.502 11795 Z= 0.313 Chirality : 0.039 0.403 1441 Planarity : 0.003 0.033 882 Dihedral : 22.924 171.857 3043 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.91 % Allowed : 19.13 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.37), residues: 513 helix: 1.19 (0.39), residues: 181 sheet: -1.11 (0.57), residues: 59 loop : -1.68 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 456 TYR 0.009 0.001 TYR A 76 PHE 0.009 0.001 PHE A 596 TRP 0.014 0.003 TRP A 452 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 8156) covalent geometry : angle 0.53026 / 0.31 (11795) hydrogen bonds : bond 0.04434 / 3.02 ( 330) hydrogen bonds : angle 3.46541 / 2.44 ( 767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 453 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8029 (mtp85) REVERT: A 610 LYS cc_start: 0.7656 (tptp) cc_final: 0.7454 (tptp) REVERT: A 699 ARG cc_start: 0.8320 (ttm110) cc_final: 0.8105 (mtm-85) REVERT: A 735 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8403 (m) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.1254 time to fit residues: 10.1286 Evaluate side-chains 59 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 44 optimal weight: 0.3980 chunk 58 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.139187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093422 restraints weight = 14896.399| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.16 r_work: 0.3118 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8156 Z= 0.138 Angle : 0.543 8.578 11795 Z= 0.315 Chirality : 0.040 0.413 1441 Planarity : 0.003 0.033 882 Dihedral : 22.843 169.547 3043 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.91 % Allowed : 19.37 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.38), residues: 513 helix: 1.28 (0.40), residues: 180 sheet: -0.98 (0.57), residues: 59 loop : -1.58 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.008 0.001 TYR A 76 PHE 0.013 0.001 PHE A 307 TRP 0.017 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 8156) covalent geometry : angle 0.54293 / 0.32 (11795) hydrogen bonds : bond 0.04561 / 3.05 ( 330) hydrogen bonds : angle 3.43385 / 2.41 ( 767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8324 (m-80) cc_final: 0.7980 (m-80) REVERT: A 185 GLU cc_start: 0.3414 (OUTLIER) cc_final: 0.2425 (tm-30) REVERT: A 203 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8341 (tm-30) REVERT: A 453 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8042 (mtp85) REVERT: A 699 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8131 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1284 time to fit residues: 9.6727 Evaluate side-chains 61 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 40 optimal weight: 0.4980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.140203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097330 restraints weight = 15028.562| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.12 r_work: 0.3104 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8156 Z= 0.124 Angle : 0.524 8.326 11795 Z= 0.305 Chirality : 0.038 0.408 1441 Planarity : 0.003 0.032 882 Dihedral : 22.817 169.652 3043 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.42 % Allowed : 20.34 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.38), residues: 513 helix: 1.28 (0.39), residues: 180 sheet: -0.95 (0.56), residues: 59 loop : -1.64 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 456 TYR 0.008 0.001 TYR A 76 PHE 0.011 0.001 PHE A 307 TRP 0.016 0.003 TRP A 452 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 8156) covalent geometry : angle 0.52367 / 0.30 (11795) hydrogen bonds : bond 0.04325 / 2.88 ( 330) hydrogen bonds : angle 3.35738 / 2.37 ( 767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8321 (m-80) cc_final: 0.7984 (m-80) REVERT: A 203 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8363 (tm-30) REVERT: A 453 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8130 (mtp85) REVERT: A 699 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8125 (mtm-85) outliers start: 10 outliers final: 10 residues processed: 62 average time/residue: 0.1272 time to fit residues: 10.0581 Evaluate side-chains 58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.138870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096313 restraints weight = 14961.360| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.02 r_work: 0.3084 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8156 Z= 0.157 Angle : 0.555 8.648 11795 Z= 0.318 Chirality : 0.040 0.423 1441 Planarity : 0.004 0.056 882 Dihedral : 22.789 167.936 3043 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.42 % Allowed : 20.58 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.38), residues: 513 helix: 1.31 (0.40), residues: 181 sheet: -0.83 (0.56), residues: 59 loop : -1.61 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 456 TYR 0.008 0.001 TYR A 76 PHE 0.013 0.001 PHE A 648 TRP 0.018 0.004 TRP A 452 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 ( 8156) covalent geometry : angle 0.55510 / 0.32 (11795) hydrogen bonds : bond 0.04661 / 3.10 ( 330) hydrogen bonds : angle 3.40831 / 2.39 ( 767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.29 seconds wall clock time: 33 minutes 48.78 seconds (2028.78 seconds total)