Starting phenix.real_space_refine on Thu Jul 2 07:26:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2z_43760/07_2026/8w2z_43760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2z_43760/07_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_43760/07_2026/8w2z_43760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2z_43760/07_2026/8w2z_43760.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2z_43760/07_2026/8w2z_43760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2z_43760/07_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-dev-6108/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: 1.44, per 1000 atoms: 0.19 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: 0.62 Conformation dependent library (CDL) restraints added in 267.8 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: 1.13 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: 1.47 Time building geometry restraints manager: 0.83 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=" N9 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 1.374 1.358 0.016 6.00e-03 2.78e+04 7.09e+00 ... (remaining 8151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11669 3.30 - 6.60: 107 6.60 - 9.90: 10 9.90 - 13.21: 8 13.21 - 16.51: 1 Bond angle restraints: 11795 Sorted by residual: 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 1.50e+00 4.44e-01 5.03e+01 angle pdb=" O4' G B 142 " pdb=" C1' G B 142 " pdb=" N9 G B 142 " ideal model delta sigma weight residual 108.20 117.90 -9.70 1.50e+00 4.44e-01 4.18e+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 angle pdb=" CA ARG A 37 " pdb=" CB ARG A 37 " pdb=" CG ARG A 37 " ideal model delta sigma weight residual 114.10 124.68 -10.58 2.00e+00 2.50e-01 2.80e+01 angle pdb=" C1' G B 143 " pdb=" N9 G B 143 " pdb=" C4 G B 143 " ideal model delta sigma weight residual 126.50 132.97 -6.47 1.30e+00 5.92e-01 2.48e+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 - 0.181: 1435 0.181 - 0.361: 4 0.361 - 0.542: 0 0.542 - 0.722: 1 0.722 - 0.903: 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 2.04e+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: 2.520 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- 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= 0.355 Angle : 0.894 16.507 11795 Z= 0.650 Chirality : 0.052 0.903 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 0.00485 / 0.36 ( 8156) covalent geometry : angle 0.89389 / 0.65 (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 : 0.250 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: 0.0918 time to fit residues: 6.9651 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 : 0.185 ------------------------------------------------------------------------------- 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: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.139068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093208 restraints weight = 14867.989| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.30 r_work: 0.3134 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8156 Z= 0.277 Angle : 0.664 11.036 11795 Z= 0.388 Chirality : 0.048 0.842 1441 Planarity : 0.005 0.042 882 Dihedral : 22.862 169.498 3043 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.60 % Allowed : 15.98 % Favored : 79.42 % 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: -1.21 (0.36), residues: 513 helix: 0.29 (0.37), residues: 180 sheet: -0.73 (0.68), residues: 49 loop : -1.58 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 568 TYR 0.015 0.002 TYR A 169 PHE 0.035 0.002 PHE A 648 TRP 0.017 0.003 TRP A 452 HIS 0.004 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.28 ( 8156) covalent geometry : angle 0.66448 / 0.39 (11795) hydrogen bonds : bond 0.06012 / 4.13 ( 330) hydrogen bonds : angle 4.27800 / 2.96 ( 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 77 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3668 (OUTLIER) cc_final: 0.3426 (tm-30) REVERT: A 301 ASP cc_start: 0.8780 (m-30) cc_final: 0.8578 (m-30) REVERT: A 591 LYS cc_start: 0.7375 (tttt) cc_final: 0.6339 (pptt) outliers start: 19 outliers final: 7 residues processed: 73 average time/residue: 0.0915 time to fit residues: 8.6606 Evaluate side-chains 58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 735 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: 20.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 = 0.140539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098050 restraints weight = 14833.078| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.98 r_work: 0.3128 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8156 Z= 0.165 Angle : 0.572 10.804 11795 Z= 0.339 Chirality : 0.043 0.758 1441 Planarity : 0.004 0.029 882 Dihedral : 22.880 171.052 3043 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.42 % Allowed : 16.95 % Favored : 80.63 % 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 (0.37), residues: 513 helix: 0.87 (0.39), residues: 180 sheet: -0.83 (0.67), residues: 49 loop : -1.54 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 568 TYR 0.008 0.001 TYR A 169 PHE 0.013 0.002 PHE A 648 TRP 0.007 0.002 TRP A 452 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 8156) covalent geometry : angle 0.57217 / 0.34 (11795) hydrogen bonds : bond 0.05074 / 3.47 ( 330) hydrogen bonds : angle 3.92942 / 2.75 ( 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 61 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.218 Fit side-chains REVERT: A 185 GLU cc_start: 0.3521 (OUTLIER) cc_final: 0.3257 (tm-30) REVERT: A 301 ASP cc_start: 0.8788 (m-30) cc_final: 0.8557 (m-30) REVERT: A 591 LYS cc_start: 0.7445 (tttt) cc_final: 0.6492 (pptt) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1111 time to fit residues: 8.2292 Evaluate side-chains 55 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.138493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096188 restraints weight = 15032.541| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.19 r_work: 0.3066 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1535 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= 0.224 Angle : 0.596 11.006 11795 Z= 0.351 Chirality : 0.045 0.807 1441 Planarity : 0.004 0.030 882 Dihedral : 22.837 169.332 3043 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.39 % Allowed : 17.43 % 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: -0.88 (0.37), residues: 513 helix: 1.00 (0.39), residues: 181 sheet: -0.83 (0.65), residues: 49 loop : -1.68 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 568 TYR 0.011 0.001 TYR A 169 PHE 0.021 0.002 PHE A 648 TRP 0.016 0.004 TRP A 452 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 ( 8156) covalent geometry : angle 0.59572 / 0.35 (11795) hydrogen bonds : bond 0.05376 / 3.65 ( 330) hydrogen bonds : angle 3.76630 / 2.63 ( 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 65 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.200 Fit side-chains REVERT: A 185 GLU cc_start: 0.3462 (OUTLIER) cc_final: 0.3158 (tm-30) REVERT: A 580 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6071 (mp0) REVERT: A 591 LYS cc_start: 0.7538 (tttt) cc_final: 0.6625 (pptt) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.0993 time to fit residues: 7.7645 Evaluate side-chains 58 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET 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 568 ARG Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.139086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092792 restraints weight = 15035.727| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.26 r_work: 0.3105 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1660 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= 0.168 Angle : 0.546 10.822 11795 Z= 0.328 Chirality : 0.043 0.761 1441 Planarity : 0.004 0.029 882 Dihedral : 22.862 171.035 3043 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.15 % Allowed : 19.13 % 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: -0.77 (0.38), residues: 513 helix: 1.21 (0.39), residues: 180 sheet: -1.07 (0.62), residues: 56 loop : -1.63 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 568 TYR 0.007 0.001 TYR A 670 PHE 0.017 0.002 PHE A 263 TRP 0.013 0.003 TRP A 452 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 ( 8156) covalent geometry : angle 0.54587 / 0.33 (11795) hydrogen bonds : bond 0.04762 / 3.26 ( 330) hydrogen bonds : angle 3.63230 / 2.54 ( 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 65 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.191 Fit side-chains REVERT: A 185 GLU cc_start: 0.3464 (OUTLIER) cc_final: 0.3222 (tm-30) REVERT: A 203 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 453 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.7932 (mtp85) REVERT: A 580 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5906 (mp0) REVERT: A 591 LYS cc_start: 0.7671 (tttt) cc_final: 0.6815 (pptt) outliers start: 13 outliers final: 8 residues processed: 62 average time/residue: 0.1090 time to fit residues: 8.6130 Evaluate side-chains 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 568 ARG Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 39 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 overall best weight: 1.0170 ------------------------------------------------------------------------------- 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 = 0.139828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093755 restraints weight = 14976.808| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.24 r_work: 0.3124 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8156 Z= 0.141 Angle : 0.526 10.557 11795 Z= 0.317 Chirality : 0.041 0.723 1441 Planarity : 0.003 0.028 882 Dihedral : 22.840 170.914 3043 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -0.70 (0.37), residues: 513 helix: 1.29 (0.39), residues: 181 sheet: -1.01 (0.60), residues: 56 loop : -1.62 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 568 TYR 0.006 0.001 TYR A 660 PHE 0.010 0.001 PHE A 648 TRP 0.014 0.003 TRP A 452 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 8156) covalent geometry : angle 0.52589 / 0.32 (11795) hydrogen bonds : bond 0.04449 / 3.03 ( 330) hydrogen bonds : angle 3.51252 / 2.47 ( 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 68 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.165 Fit side-chains REVERT: A 185 GLU cc_start: 0.3435 (OUTLIER) cc_final: 0.3220 (tm-30) REVERT: A 203 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 453 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.8019 (mtp85) REVERT: A 580 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5751 (mp0) REVERT: A 591 LYS cc_start: 0.7723 (tttt) cc_final: 0.6168 (tmmt) outliers start: 12 outliers final: 7 residues processed: 64 average time/residue: 0.1236 time to fit residues: 9.7622 Evaluate side-chains 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 580 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 696 LEU 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: 1.9990 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093588 restraints weight = 14851.623| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.30 r_work: 0.3017 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8156 Z= 0.288 Angle : 0.657 11.399 11795 Z= 0.381 Chirality : 0.049 0.908 1441 Planarity : 0.005 0.048 882 Dihedral : 22.877 166.494 3043 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % 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: -1.09 (0.37), residues: 513 helix: 1.07 (0.39), residues: 180 sheet: -1.11 (0.57), residues: 60 loop : -1.96 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 568 TYR 0.014 0.002 TYR A 169 PHE 0.025 0.002 PHE A 648 TRP 0.017 0.004 TRP A 452 HIS 0.007 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.29 ( 8156) covalent geometry : angle 0.65728 / 0.38 (11795) hydrogen bonds : bond 0.06226 / 4.15 ( 330) hydrogen bonds : angle 3.73643 / 2.59 ( 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 69 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8424 (m-80) cc_final: 0.8035 (m-80) REVERT: A 185 GLU cc_start: 0.3746 (OUTLIER) cc_final: 0.2779 (tm-30) REVERT: A 203 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 453 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.7982 (mtp85) REVERT: A 591 LYS cc_start: 0.7860 (tttt) cc_final: 0.6350 (tmmt) REVERT: A 735 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8662 (m) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.1163 time to fit residues: 9.6008 Evaluate side-chains 67 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.138893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092561 restraints weight = 14942.867| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.19 r_work: 0.3107 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2132 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= 0.131 Angle : 0.538 10.729 11795 Z= 0.322 Chirality : 0.042 0.744 1441 Planarity : 0.003 0.029 882 Dihedral : 22.933 170.789 3043 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.18 % Allowed : 20.10 % 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: -0.79 (0.37), residues: 513 helix: 1.22 (0.40), residues: 180 sheet: -0.80 (0.63), residues: 53 loop : -1.73 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 460 TYR 0.006 0.001 TYR A 76 PHE 0.012 0.001 PHE A 307 TRP 0.015 0.003 TRP A 452 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 8156) covalent geometry : angle 0.53761 / 0.32 (11795) hydrogen bonds : bond 0.04496 / 3.07 ( 330) hydrogen bonds : angle 3.51917 / 2.47 ( 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 69 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3455 (OUTLIER) cc_final: 0.2523 (tm-30) REVERT: A 203 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 453 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8062 (mtp85) REVERT: A 574 GLU cc_start: 0.6922 (tp30) cc_final: 0.6619 (tp30) REVERT: A 591 LYS cc_start: 0.7974 (tttt) cc_final: 0.6596 (tmmt) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.1053 time to fit residues: 8.8417 Evaluate side-chains 63 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.0670 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 overall best weight: 1.1120 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092497 restraints weight = 14866.412| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.17 r_work: 0.3107 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8156 Z= 0.149 Angle : 0.539 10.611 11795 Z= 0.321 Chirality : 0.042 0.741 1441 Planarity : 0.004 0.028 882 Dihedral : 22.851 168.481 3043 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.18 % Allowed : 20.34 % 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: -0.73 (0.38), residues: 513 helix: 1.26 (0.40), residues: 180 sheet: -0.94 (0.57), residues: 58 loop : -1.64 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 453 TYR 0.006 0.001 TYR A 76 PHE 0.011 0.001 PHE A 648 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 0.00284 / 0.15 ( 8156) covalent geometry : angle 0.53912 / 0.32 (11795) hydrogen bonds : bond 0.04565 / 3.08 ( 330) hydrogen bonds : angle 3.46597 / 2.43 ( 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 65 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8361 (m-80) cc_final: 0.8008 (m-80) REVERT: A 185 GLU cc_start: 0.3495 (OUTLIER) cc_final: 0.2505 (tm-30) REVERT: A 203 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 453 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8118 (mtp85) REVERT: A 574 GLU cc_start: 0.6967 (tp30) cc_final: 0.6635 (tp30) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.1062 time to fit residues: 8.5207 Evaluate side-chains 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 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 583 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 40 optimal weight: 0.9980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.139554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096544 restraints weight = 15064.262| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.18 r_work: 0.3091 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8156 Z= 0.131 Angle : 0.534 10.337 11795 Z= 0.317 Chirality : 0.041 0.703 1441 Planarity : 0.004 0.064 882 Dihedral : 22.849 169.014 3043 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.94 % Allowed : 20.82 % 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: -0.69 (0.37), residues: 513 helix: 1.27 (0.39), residues: 180 sheet: -0.84 (0.57), residues: 58 loop : -1.62 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 460 TYR 0.007 0.001 TYR A 76 PHE 0.012 0.001 PHE A 307 TRP 0.019 0.004 TRP A 452 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 8156) covalent geometry : angle 0.53410 / 0.32 (11795) hydrogen bonds : bond 0.04283 / 2.88 ( 330) hydrogen bonds : angle 3.41742 / 2.41 ( 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 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8364 (m-80) cc_final: 0.8001 (m-80) REVERT: A 185 GLU cc_start: 0.3488 (OUTLIER) cc_final: 0.2532 (tm-30) REVERT: A 203 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 453 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8202 (mtp85) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.1055 time to fit residues: 7.8276 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 : 0.140 ------------------------------------------------------------------------------- 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 583 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 692 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 59 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087606 restraints weight = 14878.032| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.45 r_work: 0.3008 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 8156 Z= 0.345 Angle : 0.729 11.767 11795 Z= 0.415 Chirality : 0.053 0.992 1441 Planarity : 0.006 0.051 882 Dihedral : 22.902 165.697 3043 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.94 % Allowed : 21.31 % Favored : 76.76 % 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: -1.15 (0.37), residues: 513 helix: 0.78 (0.39), residues: 180 sheet: -0.94 (0.57), residues: 61 loop : -1.86 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 456 TYR 0.015 0.002 TYR A 588 PHE 0.027 0.002 PHE A 648 TRP 0.019 0.004 TRP A 452 HIS 0.005 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.34 ( 8156) covalent geometry : angle 0.72950 / 0.42 (11795) hydrogen bonds : bond 0.07107 / 4.68 ( 330) hydrogen bonds : angle 3.88429 / 2.70 ( 767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.59 seconds wall clock time: 29 minutes 6.67 seconds (1746.67 seconds total)