Starting phenix.real_space_refine on Wed Sep 17 09:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_43760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_43760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_43760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_43760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2z_43760/09_2025/8w2z_43760.map" } 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-2.0-5805/lib/python3.9/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: 2.04, per 1000 atoms: 0.27 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: 0.70 Conformation dependent library (CDL) restraints added in 315.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.24 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: 1.59 Time building geometry restraints manager: 0.90 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 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.90e+00 bond pdb=" C3' U B 92 " pdb=" O3' U B 92 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.53e+00 bond pdb=" CB GLU A 723 " pdb=" CG GLU A 723 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" C2' G B 142 " pdb=" C1' G B 142 " ideal model delta sigma weight residual 1.526 1.504 0.022 1.50e-02 4.44e+03 2.06e+00 bond pdb=" CA ARG A 37 " pdb=" C ARG A 37 " ideal model delta sigma weight residual 1.523 1.542 -0.020 1.41e-02 5.03e+03 1.94e+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=" CA ARG A 229 " pdb=" CB ARG A 229 " pdb=" CG ARG A 229 " ideal model delta sigma weight residual 114.10 124.05 -9.95 2.00e+00 2.50e-01 2.47e+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 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.51e+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: 2.680 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.073 8156 Z= 0.210 Angle : 0.870 16.507 11795 Z= 0.455 Chirality : 0.050 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 aren 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 covalent geometry : bond 0.00452 ( 8156) covalent geometry : angle 0.87016 (11795) hydrogen bonds : bond 0.11310 ( 330) hydrogen bonds : angle 5.11272 ( 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 : 0.231 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: 0.1137 time to fit residues: 8.5530 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 : 0.233 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.137507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096287 restraints weight = 14847.836| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.99 r_work: 0.3074 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8156 Z= 0.295 Angle : 0.701 10.388 11795 Z= 0.379 Chirality : 0.046 0.817 1441 Planarity : 0.005 0.032 882 Dihedral : 22.750 167.130 3043 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.87 % Allowed : 15.74 % Favored : 80.39 % 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 aren not related in a simple way. whole: -1.25 (0.36), residues: 513 helix: 0.31 (0.38), residues: 181 sheet: -0.88 (0.62), residues: 59 loop : -1.64 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 568 TYR 0.013 0.002 TYR A 169 PHE 0.026 0.002 PHE A 648 TRP 0.016 0.003 TRP A 452 HIS 0.005 0.002 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 8156) covalent geometry : angle 0.70117 (11795) hydrogen bonds : bond 0.05357 ( 330) hydrogen bonds : angle 4.08174 ( 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 76 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3678 (OUTLIER) cc_final: 0.3367 (tm-30) REVERT: A 591 LYS cc_start: 0.7505 (tttt) cc_final: 0.6586 (pptt) outliers start: 16 outliers final: 7 residues processed: 72 average time/residue: 0.1300 time to fit residues: 11.9060 Evaluate side-chains 57 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098388 restraints weight = 14816.742| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.94 r_work: 0.3108 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8156 Z= 0.166 Angle : 0.589 9.692 11795 Z= 0.323 Chirality : 0.041 0.738 1441 Planarity : 0.004 0.029 882 Dihedral : 22.700 169.810 3043 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.66 % Allowed : 18.89 % Favored : 78.45 % 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 aren not related in a simple way. whole: -0.77 (0.38), residues: 513 helix: 0.96 (0.39), residues: 181 sheet: -0.83 (0.66), residues: 56 loop : -1.49 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 456 TYR 0.008 0.001 TYR A 169 PHE 0.015 0.002 PHE A 235 TRP 0.012 0.002 TRP A 452 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8156) covalent geometry : angle 0.58884 (11795) hydrogen bonds : bond 0.04017 ( 330) hydrogen bonds : angle 3.67443 ( 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 66 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 456 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8420 (tmm-80) REVERT: A 580 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: A 591 LYS cc_start: 0.7637 (tttt) cc_final: 0.6825 (pptt) REVERT: A 598 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8349 (ttm170) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1406 time to fit residues: 11.1816 Evaluate side-chains 56 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089874 restraints weight = 14980.570| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.32 r_work: 0.3057 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8156 Z= 0.279 Angle : 0.664 10.554 11795 Z= 0.361 Chirality : 0.046 0.859 1441 Planarity : 0.004 0.031 882 Dihedral : 22.736 167.510 3043 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.87 % Allowed : 17.92 % Favored : 78.21 % 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 aren not related in a simple way. whole: -0.89 (0.38), residues: 513 helix: 1.04 (0.40), residues: 181 sheet: -0.95 (0.60), residues: 61 loop : -1.70 (0.38), residues: 271 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 0.014 0.003 TRP A 452 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 8156) covalent geometry : angle 0.66353 (11795) hydrogen bonds : bond 0.05019 ( 330) hydrogen bonds : angle 3.68391 ( 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 73 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8324 (m-80) cc_final: 0.7937 (m-80) REVERT: A 185 GLU cc_start: 0.3662 (OUTLIER) cc_final: 0.2588 (tm-30) REVERT: A 203 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 456 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8426 (tmm-80) REVERT: A 574 GLU cc_start: 0.7135 (tp30) cc_final: 0.6750 (tp30) REVERT: A 588 TYR cc_start: 0.7528 (m-80) cc_final: 0.7191 (m-80) REVERT: A 591 LYS cc_start: 0.7989 (tttt) cc_final: 0.6590 (tmmt) REVERT: A 735 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8537 (m) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.1225 time to fit residues: 10.7709 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 : 0.122 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 41 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 overall best weight: 0.9258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093427 restraints weight = 15039.961| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.20 r_work: 0.3119 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8156 Z= 0.143 Angle : 0.559 9.125 11795 Z= 0.308 Chirality : 0.039 0.697 1441 Planarity : 0.003 0.029 882 Dihedral : 22.657 168.269 3043 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.66 % Allowed : 19.61 % 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 aren not related in a simple way. whole: -0.62 (0.38), residues: 513 helix: 1.30 (0.40), residues: 182 sheet: -0.57 (0.64), residues: 54 loop : -1.63 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 568 TYR 0.006 0.001 TYR A 169 PHE 0.014 0.001 PHE A 235 TRP 0.014 0.003 TRP A 452 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8156) covalent geometry : angle 0.55877 (11795) hydrogen bonds : bond 0.03652 ( 330) hydrogen bonds : angle 3.35063 ( 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 66 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 699 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8119 (mtm-85) REVERT: A 735 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (m) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.1277 time to fit residues: 10.2951 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 : 0.213 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 735 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.138013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.094780 restraints weight = 14971.953| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.07 r_work: 0.3059 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.004 0.052 8156 Z= 0.194 Angle : 0.596 9.817 11795 Z= 0.327 Chirality : 0.042 0.769 1441 Planarity : 0.004 0.030 882 Dihedral : 22.630 165.641 3043 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.66 % Allowed : 19.37 % 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 aren not related in a simple way. whole: -0.64 (0.38), residues: 513 helix: 1.30 (0.40), residues: 181 sheet: -0.78 (0.58), residues: 59 loop : -1.60 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.007 0.001 TYR A 169 PHE 0.014 0.001 PHE A 648 TRP 0.014 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8156) covalent geometry : angle 0.59563 (11795) hydrogen bonds : bond 0.04077 ( 330) hydrogen bonds : angle 3.38647 ( 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 65 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.8354 (m-80) cc_final: 0.7953 (m-80) REVERT: A 185 GLU cc_start: 0.3415 (OUTLIER) cc_final: 0.2291 (tm-30) REVERT: A 203 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8373 (tm-30) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1157 time to fit residues: 9.4029 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 : 0.250 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091886 restraints weight = 14878.798| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.26 r_work: 0.3003 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8156 Z= 0.262 Angle : 0.651 10.348 11795 Z= 0.354 Chirality : 0.045 0.862 1441 Planarity : 0.004 0.042 882 Dihedral : 22.708 165.438 3043 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.91 % Allowed : 19.61 % 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 aren not related in a simple way. whole: -0.80 (0.37), residues: 513 helix: 1.13 (0.40), residues: 181 sheet: -0.84 (0.57), residues: 61 loop : -1.69 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 37 TYR 0.009 0.002 TYR A 169 PHE 0.018 0.002 PHE A 648 TRP 0.015 0.003 TRP A 452 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8156) covalent geometry : angle 0.65116 (11795) hydrogen bonds : bond 0.04860 ( 330) hydrogen bonds : angle 3.51154 ( 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 66 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.2612 (tm-30) REVERT: A 203 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8395 (tm-30) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.1065 time to fit residues: 8.8438 Evaluate side-chains 60 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 178 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092007 restraints weight = 15063.982| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.31 r_work: 0.3007 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8156 Z= 0.234 Angle : 0.627 9.848 11795 Z= 0.340 Chirality : 0.044 0.821 1441 Planarity : 0.004 0.059 882 Dihedral : 22.690 166.011 3043 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % 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 aren not related in a simple way. whole: -0.82 (0.37), residues: 513 helix: 1.13 (0.39), residues: 182 sheet: -0.81 (0.57), residues: 61 loop : -1.73 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 460 TYR 0.009 0.002 TYR A 95 PHE 0.016 0.002 PHE A 648 TRP 0.015 0.003 TRP A 452 HIS 0.003 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8156) covalent geometry : angle 0.62709 (11795) hydrogen bonds : bond 0.04418 ( 330) hydrogen bonds : angle 3.45921 ( 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 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.3760 (OUTLIER) cc_final: 0.2765 (tm-30) REVERT: A 582 ASP cc_start: 0.8133 (t0) cc_final: 0.7894 (t0) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.1191 time to fit residues: 9.6245 Evaluate side-chains 57 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 178 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.0010 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095160 restraints weight = 15001.331| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.18 r_work: 0.3057 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8156 Z= 0.139 Angle : 0.569 8.854 11795 Z= 0.311 Chirality : 0.039 0.691 1441 Planarity : 0.005 0.092 882 Dihedral : 22.600 165.594 3043 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % 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 aren not related in a simple way. whole: -0.56 (0.37), residues: 513 helix: 1.33 (0.40), residues: 182 sheet: -0.72 (0.59), residues: 59 loop : -1.55 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 460 TYR 0.007 0.001 TYR A 588 PHE 0.013 0.001 PHE A 570 TRP 0.017 0.003 TRP A 452 HIS 0.002 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8156) covalent geometry : angle 0.56858 (11795) hydrogen bonds : bond 0.03585 ( 330) hydrogen bonds : angle 3.26658 ( 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: 10 poor density : 55 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 460 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: A 582 ASP cc_start: 0.8007 (t0) cc_final: 0.7695 (t0) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1222 time to fit residues: 9.9155 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 178 ILE 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 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: 5.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.139175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097958 restraints weight = 15197.460| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.97 r_work: 0.3088 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8156 Z= 0.136 Angle : 0.560 8.974 11795 Z= 0.307 Chirality : 0.039 0.683 1441 Planarity : 0.004 0.070 882 Dihedral : 22.522 165.145 3043 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.18 % Allowed : 20.82 % 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 aren not related in a simple way. whole: -0.33 (0.38), residues: 513 helix: 1.54 (0.40), residues: 180 sheet: -0.14 (0.62), residues: 54 loop : -1.50 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 460 TYR 0.006 0.001 TYR A 76 PHE 0.011 0.001 PHE A 570 TRP 0.019 0.004 TRP A 452 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8156) covalent geometry : angle 0.56002 (11795) hydrogen bonds : bond 0.03551 ( 330) hydrogen bonds : angle 3.21082 ( 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 61 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7003 (mp0) cc_final: 0.5970 (mp0) REVERT: A 582 ASP cc_start: 0.7981 (t0) cc_final: 0.7709 (t0) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1127 time to fit residues: 8.6812 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 : 0.205 ------------------------------------------------------------------------------- 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 649 LYS 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: 5.9990 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.090377 restraints weight = 14861.471| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.36 r_work: 0.2981 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3258 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= 0.308 Angle : 0.703 10.504 11795 Z= 0.378 Chirality : 0.047 0.895 1441 Planarity : 0.005 0.071 882 Dihedral : 22.663 166.518 3043 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.18 % Allowed : 20.82 % 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 aren not related in a simple way. whole: -0.73 (0.37), residues: 513 helix: 1.10 (0.40), residues: 181 sheet: -0.52 (0.59), residues: 61 loop : -1.64 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 456 TYR 0.013 0.002 TYR A 95 PHE 0.021 0.002 PHE A 648 TRP 0.020 0.004 TRP A 452 HIS 0.005 0.002 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 8156) covalent geometry : angle 0.70345 (11795) hydrogen bonds : bond 0.05376 ( 330) hydrogen bonds : angle 3.59222 ( 767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.90 seconds wall clock time: 32 minutes 51.92 seconds (1971.92 seconds total)